Basics Manual

SYBYL®-X 2.1
Mid 2013

1699 South Hanley Rd. Phone: +1.314.647.1099

St. Louis, MO Fax: +1.314.647.9241
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following patents: AllChem: US 7,860,657; Comparative Molecular Field Analysis (CoMFA): US 5,025,388; US
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 SYBYL Basics Table of Contents

1. Introduction to SYBYL Basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

1.1 What is New with SYBYL Basics Features . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.2 License Requirements for SYBYL Basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

2. Quick Introduction to SYBYL-X . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

2.1 Start SYBYL-X . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.2 Load Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.3 Rotate, Translate, and Scale Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.4 Save a Molecule to a File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.5 Get Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.6 Exit SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
2.7 Starting SYBYL-X and Setting its Environment . . . . . . . . . . . . . . . . . . . . . . 23

3. The SYBYL Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

3.1 The SYBYL Menubar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.2 The SYBYL Toolbar Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
3.3 The SYBYL Textports and Consoles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
3.4 Special Keyboard Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

4. Read and Write Files of Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

4.1 Import (Read) Molecules From Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
4.2 Export (Write) Molecules to Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
4.3 Molecule File Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
4.4 Convert Between Molecular File Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

5. Understand Molecule and Display Areas . . . . . . . . . . . . . . . . . . . . . . . . . . 55

6. Select Atoms, Bonds, or Substructures . . . . . . . . . . . . . . . . . . . . . . . . . . 57

6.1 Selecting With the Mouse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
6.2 The Selection Menu and Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
6.3 General Description of the Expression Dialogs . . . . . . . . . . . . . . . . . . . . . . . 64
6.4 How to Use the Atom Expression Dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
6.5 How to Use the Bond Expression dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
6.6 How to Use the Substructure Expression Dialog . . . . . . . . . . . . . . . . . . . . . . 82

7. Clear and Reset the SYBYL Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

7.1 Clear the SYBYL Screen and Delete Objects . . . . . . . . . . . . . . . . . . . . . . . . 86
7.2 Reset Scaling, Translation, and Rotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
7.3 Undo the Last Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

8. The SYBYL Sketcher . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93

8.1 Sketch a Small Molecule Tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
8.2 Access the Sketcher . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101

SYBYL-X 2.1 SYBYL Basics 3

 8.3 Sketcher Toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105

9. Molecules: Build, Delete, Modify . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .109

9.1 Copy or Move Atoms Between Molecule Areas . . . . . . . . . . . . . . . . . . . . . 110
9.2 Combine Two Molecules Into One . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
9.3 Delete a Molecule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
9.4 Name or Rename a Molecule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
9.5 Chirality: Determine and Modify . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
9.6 Modify Molecule Attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128

10. Substructures: Delete, Modify . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .131

10.1 Delete Substructures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
10.2 Modify Substructures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133

11. Atoms: Add, Delete, Modify . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .135

11.1 Add Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
11.2 Delete Atoms or Atom Attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
11.3 Modify Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141

12. Bonds: Add, Delete, Modify . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .147

12.1 Add Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
12.2 Delete Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
12.3 Modify a Bond Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151

13. Geometry: Measure, Modify, Define Features . . . . . . . . . . . . . . . . . . . .153

13.1 Geometric Measurements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
13.2 Modify Molecular Geometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
13.3 Geometric Features: Define and Modify . . . . . . . . . . . . . . . . . . . . . . . . . . 159

14. Get Information on SYBYL Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . .169

14.1 Definitions of SYBYL Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
14.2 Information on individual Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
14.3 List Information About SYBYL Objects . . . . . . . . . . . . . . . . . . . . . . . . . . 175
14.4 Print Information About Objects to a File . . . . . . . . . . . . . . . . . . . . . . . . . 176

15. Use Molecule Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .177

15.1 Database Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
15.2 Open and Close SYBYL Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
15.3 Retrieve Molecules from a SYBYL Database . . . . . . . . . . . . . . . . . . . . . . 182
15.4 Obtain Information on Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
15.5 Manage Database Content . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
15.6 Save Database Molecules to Mol2 Files . . . . . . . . . . . . . . . . . . . . . . . . . . 191
15.7 Database Qualifiers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192

4 SYBYL Basics SYBYL-X 2.1

 15.8 The DATABASE Command . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
15.9 System Utilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194

16. Manage SYBYL Sessions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195

16.1 Save a SYBYL Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
16.2 Open (Restore) a Saved Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
16.3 Delete a Saved Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
16.4 Open a New Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
16.5 Close a SYBYL Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
16.6 Record and Play Back SYBYL Operations . . . . . . . . . . . . . . . . . . . . . . . . 202

17. Sets in SYBYL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207

17.1 Global Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
17.2 Local Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212
17.3 Dynamic Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214
17.4 Built-in Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
17.5 Static Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220
17.6 Working with Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221

18. Libraries of Fragments and Functional Groups . . . . . . . . . . . . . . . . . . 223

18.1 Fragment Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
18.2 Group Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229

SYBYL-X 2.1 SYBYL Basics 5

This page intentionally blank.
 1. Introduction to SYBYL Basics

SYBYL uses computer analysis to assist in the description and prediction of

molecular behavior. SYBYL Base includes the basic tools for molecular
modeling. Topics in this manual include:
• Quick Introduction to SYBYL-X on page 11
• Rotate, Translate, and Scale Molecules on page 17
• The SYBYL Window on page 27
• Read and Write Files of Molecules on page 35
• Understand Molecule and Display Areas on page 55
• Select Atoms, Bonds, or Substructures on page 57
• Clear and Reset the SYBYL Display on page 85
• The SYBYL Sketcher on page 93
• Molecules: Build, Delete, Modify on page 109
• Substructures: Delete, Modify on page 131
• Atoms: Add, Delete, Modify on page 135
• Bonds: Add, Delete, Modify on page 147
• Geometric Measurements on page 154
• Get Information on SYBYL Objects on page 169
• Use Molecule Databases on page 177
• Manage SYBYL Sessions on page 195
• Sets in SYBYL on page 207
• Libraries of Fragments and Functional Groups on page 223

When combined with SYBYL applications, SYBYL Base provides a completely

integrated environment for computational chemistry and molecular modeling.

SYBYL-X 2.1 SYBYL Basics 7

1. Introduction to SYBYL Basics
What is New with SYBYL Basics Features

1.1 What is New with SYBYL Basics Features

Display of File Extensions During Saving
In the Rotatable Bonds dialog, if a rotatable bond is deleted, any angle changes
made are ignored and the bond’s angle is reset to its original value as long as
the Apply button has not been pressed.

Save Image
File > Save Image now saves UNITY features and CoMFA fields correctly.

SLN Files with Null Values

SLN files containing a null value can now be successfully saved as a TSV
formatted file.

Deletion of Rotatable Bonds

In the Rotatable Bonds dialog, if a rotatable bond is deleted, any angle changes
made are ignored and the bond’s angle is reset to its original value as long as
the Apply button has not been pressed.

An issue involving the reappearance of deleted rotatable bonds when the

Rotatable Bonds dialog is redisplayed has been resolved.

PDB Retrieval from RCSB Server

Updates to the RCSB Server caused problems with SYBYL’s ability to retrieve
PDB files. This issue has been resolved.

8 SYBYL Basics SYBYL-X 2.1

 1. Introduction to SYBYL Basics
License Requirements for SYBYL Basics

1.2 License Requirements for SYBYL Basics

SYBYL-X Suite Licensing

SYBYL-X introduced a simplified licensing scheme in which the “SYBYL”

license provides access to all functionality described in this manual.

Two additional keys perform the following functions:

• SYBYL_Interactive: Controls interactive access to SYBYL and other
programs
• CPU: Allows remote operations

Module-Based Licensing

SYBYL continues to run with a license file issued before the SYBYL-X release.
The functionality described in this manual requires a “SybylBasic” license.

Additionally, a “BioPolymer” license:

• is required to assign and label AMBER and Kollman atom types;
• is used, if present, to add hydrogens to proteins, nucleic acids and
saccharides.

SYBYL-X 2.1 SYBYL Basics 9

This page intentionally blank.
 2. Quick Introduction to SYBYL-X

Run this tutorial to learn some basics operations in SYBYL:

• Start SYBYL-X on page 12
• Load Molecules on page 16
• Change the Display on page 16
• Rotate, Translate, and Scale Molecules on page 17
• Save a Molecule to a File on page 20
• Get Help on page 21
• Exit SYBYL on page 22
• Starting SYBYL-X and Setting its Environment on page 23

A Matter of Time: This tutorial requires about 5 minutes of personal time.

SYBYL-X 2.1 SYBYL Basics 11

2. Quick Introduction to SYBYL-X
Start SYBYL-X

2.1 Start SYBYL-X

Windows Users:
! Double-click the SYBYL-X 2.1 icon on your desktop or find SYBYL-X
2.1 in your computer’s All Programs list.

Linux Users:
! If there is a SYBYL-X 2.1 icon on your desktop, double-click it.

! Otherwise open a system shell then start the SYBYL-X program by

typing (replacing $TA_ROOT with its full path):
$TA_ROOT/sybyl -shell

Mac Users:
! If SYBYL-X 2.1 is in your Dock, double-click it.

Or, if SYBYL-X 2.1 was installed “for all users”:

! In the Finder’s Go menu select Applications, then SYBYL-X 2.1.

Double-click on SYBYL-X.

Or, if SYBYL-X 2.1 was installed by a single user with no administrator

privilege:

! In the Finder’s Go menu select Home, then bin, then SYBYL-X 2.1.
Double-click on SYBYL-X.

SYBYL Session
A SYBYL session begins when you start SYBYL and ends when you close it.
The current state of a SYBYL session can be saved and reloaded at a later time.
You may also run multiple sessions simultaneously. See Manage SYBYL
Sessions on page 195 for more details.

12 SYBYL Basics SYBYL-X 2.1

 2. Quick Introduction to SYBYL-X
Start SYBYL-X

Explore the SYBYL Window

The SYBYL graphical interface is composed of a menubar, toolbar icons, a
graphics area, a command console, a system message area, and a job control
area.

Menubar
A SYBYL menu option can:
• be a simple command: Edit > Delete Everything
• lead to submenus: Biopolymer > Model Proteins > ORCHESTRAR
• open a dialog: File > Import File...

Each list of menu options can be detached from the menubar so that it remains
visible even after a selection is made.
• To detach a menu: click the dashed line above the first item.
• To close a tear-off: click the X in the upper right corner.

When you initiate an operation by clicking a menu item, no other operation is

possible until either that operation completes or you cancel it. All menubars are
greyed out while the current operation is active.

SYBYL-X 2.1 SYBYL Basics 13

2. Quick Introduction to SYBYL-X
Start SYBYL-X

Additional Information:
• The SYBYL Menubar on page 28
• Menu, Dialog, and Mouse Shortcuts on page 29

Toolbars
Use the icons in the SYBYL toolbars to interact with the graphics. Clicking
some icons immediately performs an action, others require a selection to be
made from a pull-down, and others display a tool that can remain open as you
work or can be closed by pressing the X button in the corner of its window.

Each toolbar can be docked under the menubar or to either side of the display
area or “torn off” so that it exists in its own window. To move a toolbar click its
grab line and drag it to the desired location.

Command Console
Use this console to enter any command at the SYBYL command prompt
(SYBYL>). After entering a command, the system performs the command
operation and redisplays the SYBYL command prompt. See the List of SYBYL
Commands in the SYBYL Reference Guide.

Note: The menubar and command line are available simultaneously.

System Messages
A few SYBYL operations report information in this area. You may also type
simple system commands in the Command Console (e.g. cmd ls to list the files
in the current directory or folder). The output of such a command appears in the
System Messages area.

See The SYBYL Window on page 27 for more in-depth description of the
SYBYL interface.

Job Control
This console monitors jobs that have been submitted either to run in the
background on the local machine or to run remotely. Use the button terminate a
selected process. You may also remove a process from the list (note that this
does not kill the process, only removes the item from the displayed list), display
process information, or refresh the list. Instructions for Job Control setup can be
found at https://tools.certara.com/confluence/display/SYB/Job+Control.

Status Bar
A single text line at the bottom of the SYBYL window reflects the current state
of two important elements of SYBYL:
1. The default molecule area. Most often this will be M1.
When multiple molecule areas are occupied, the default molecule area is the
one that is automatically selected in various dialogs.

14 SYBYL Basics SYBYL-X 2.1

 2. Quick Introduction to SYBYL-X
Start SYBYL-X

2. The full path to the current working directory/folder. By default this is your
“Home” directory or folder unless you started SYBYL from a different
location.

You may change the location of the default directory within SYBYL via
Options > Set > Default Directory.

If you have a preferred location to store files related to your SYBYL projects
you may specify it in your personal startup file, the sybyl.ini file.
1. Make sure that the desired directory or folder exists.
2. Create a text file that contains the following SYBYL command:
set default_directory <full path to the desired directory or folder>
3. Name the file sybyl.ini and place it in your HOME directory.
• On linux and Mac: HOME is the directory you are in upon opening a
terminal window.
• On Windows HOME is:
• Windows XP: your Documents and Settings/user folder
• Windows 7: your Users/username folder

Refer to The sybyl.ini File in the Customizing SYBYL section of the Tripos
Bookshelf for details and for a sample file.

SYBYL-X 2.1 SYBYL Basics 15

2. Quick Introduction to SYBYL-X
Load Molecules

2.2 Load Molecules

Molecules can be loaded into SYBYL from files. A Fragment Library is also
available, containing a number of small, mostly cyclic, molecules.

2.2.1 Load a Molecule from a File

Read in dicloxacillin from a list of demo files distributed with SYBYL.

! Click (or File > Import File).

! In the Open File dialog, click [$TA_DEMO] in the Bookmarks section

on the left.

The contents of SYBYL’s demo directory are displayed in the sections on the
right.

! Select example.mdb in the Directory Navigation list in the center.

! Double-click dicloxacillin.mol2 in the Selection list on the right.

SYBYL loads dicloxacillin into M1, the default molecule area if you started
with a blank screen. A molecule area is a region of memory that holds a
particular molecule.

2.2.2 Load a Molecule from the Fragment Library

Load vitamin B2.

! File > Get Fragment

! Select VITAMIN B2 in the list of available molecules and press OK.

SYBYL loads vitamin B2 into M2, the first empty molecule area.

Both molecules are displayed in the center of the SYBYL window. In the next
section, you will learn how to change the display so that you can see the
molecules more clearly.

2.2.3 Change the Display

1. Change the display so you can see the molecules side-by-side.

! Click and select Half.

SYBYL displays the molecules in display areas D1 (right) and D2 (left).

16 SYBYL Basics SYBYL-X 2.1

 2. Quick Introduction to SYBYL-X
Rotate, Translate, and Scale Molecules

For more information, see What are Molecule and Display Areas? on page 55.

2. Toggle the display for each molecule off and on.

! Click .

! In Molecule Display Options dialog, for row M1, toggle the check box in
the Mol Vis column off and then on.

Notice also that the check box appearance changes. Watch the SYBYL screen
when you toggle the display off and on. Likewise, the other molecule can be
displayed and undisplayed using the respective check box.

! Display both molecules and click the X in the upper corner to close
the dialog.

2.3 Rotate, Translate, and Scale Molecules

Structure rotation is based on the Cartesian coordinate system such that the
X-axis is horizontal, the Y-axis is vertical, and the Z-axis is perpendicular to the
viewer.

SYBYL supports a three-button mouse, reserving the right button for context
sensitive menus. When using a touch pad use on the Mouse Mode toolbar.

2.3.1 Move All Objects Together

Move All Objects Mouse Keyboard Mac Keyboard

X,Y rotation Left
X,Y translation Middle — Alt
Left Shift Shift
Z rotation Left Ctrl+Shift Command+Shift
Z translation Middle Ctrl Command
90° rotationa — Ctrl+arrow keys Command+arrow
keys
a. To change the rotation increment from its default of 90° use Tailor variable GRAPHICS
KEYBOARD_ARROW_ROTATION.

Linux Usage Note

If the Ctrl or Alt keys do not behave as described above it may be because of a
preference setting for your window manager. We recommend the following
setting for the Gnome window manager:
• System (or Applications) > Preference > Windows

SYBYL-X 2.1 SYBYL Basics 17

2. Quick Introduction to SYBYL-X
Rotate, Translate, and Scale Molecules

• Set Movement Key to Super (or “Windows logo”).

1. Rotate both molecules. When you start a SYBYL session all images on the
screen are affected simultaneously by rotations and translations.
! With the cursor in the graphics window, press the left mouse button
and move your mouse in any direction.
Notice that all molecules move. This is because your current mouse focus
setting is G (global), as indicated by the icon on the Mouse Mode
toolbar.

2. Rotate the molecules about the Z-axis.

! Simultaneously hold the Ctrl and Shift keys while pressing the left
button and dragging left or right.

Mac Users: Use the Command and Shift keys.

2.3.2 Move Selected Objects Only

To move one or more, but not all, objects simultaneously you must first select
them. Then add Alt to the key/mouse combination:

Move Selected Objects Mouse Keyboard

X,Y rotation Left Alt
X,Y translation Middle Alt
Left Alt+Shift
Z rotation Left Alt+Ctrl+Shift
(Mac: Alt+Command+Shift)
Z translation Rotate all objects in X,Y by 90°
then select the object(s) of interest
and translate them in the XY plane.

3. Move dicloxacillin to the upper right corner.

! Click an atom in dicloxacillin.

! Hold down the Alt and Shift keys while pressing the left button and
dragging the cursor to the upper right corner of the display area.
Vitamin B2 remains stationary.

An alternative method is to change the mouse focus using a toolbar icon.

! Clear the selection first by clicking .

18 SYBYL Basics SYBYL-X 2.1

 2. Quick Introduction to SYBYL-X
Rotate, Translate, and Scale Molecules

! Click on the toolbar.

SYBYL opens the Mouse Focus Options dialog with a list of molecules.

! Click M1 dicloxacillin.
SYBYL changes the mouse focus to M1. Note that the notation on the icon
changed from G to M1. This notation represents the active object for the
mouse focus.

! Middle-click and drag dicloxacillin to the lower right corner.

If you had multiple molecules in D1, all of those molecules would move
together. In such cases, to only move a particular molecule using this dialog,
click the name of the molecule in the list, then use the mouse.

4. Move vitamin B2 to the upper left corner.

! In the dialog click M2 vitamin B2.
SYBYL changes the mouse focus to M2 only.

! Middle-click and drag vitamin B2 to the upper left corner.

! Reset the mouse focus to Global then click X in the upper corner to
close the Mouse Focus Options dialog.

2.3.3 Zoom Objects with the Mouse

The zoom modifies the scale of all objects, whether visible or not.

Mouse Zooming Action

Wheel Scroll forward to zoom in by 5%.
Scroll backward to zoom out by 5%.
Left+Middle Drag the mouse to the upper right to zoom in.
Drag the mouse to the lower left to zoom out.
Ctrl+Left Drag the mouse to the upper right to zoom in.
Mac: Command+Left Drag the mouse to the lower left to zoom out.

5. Modify the size of the molecules.

! Use the mouse’s scroll wheel to increase the size of both molecules.

If your mouse does not have a scroll wheel use either of the alternatives
described above.

SYBYL-X 2.1 SYBYL Basics 19

2. Quick Introduction to SYBYL-X
Save a Molecule to a File

2.3.4 Reset Rotation, Translation, and Scale

All rotations, translations, and scale operations applied globally or individually
can be reset with a single click.

! Click .

2.3.5 Moving Objects in a Single Display Area

If you have four or fewer molecules in different display areas and you want to
manipulate one of them independently of the others you can toggle the mouse
focus between Global (all together) and a single one by pressing a function key.

The label of the Mouse Focus icon ( ) will reflect the current status.
• F9—toggles between Global and D1
• F10—toggles between G and D2
• F11—toggles between G and D3
• F12—toggles between G and D4
! Experiment with function keys F9 and F10 to move each molecule
independently of the other, then both together.
! Be sure to toggle the function keys back to Global when you are
done.

2.4 Save a Molecule to a File

! File > Export File ( )

SYBYL opens the Save Molecule dialog.

! Verify that m1: dicloxacillin is highlighted in the list; if not, select it.

! Type diclox_tut in the File field.

! Press Save.

SYBYL creates a file named diclox_tut.mol2 in your current directory.

Note: You can select multiple structures and save them in a specified format.
For more information, see Export (Write) Molecules to Files on page 40.

20 SYBYL Basics SYBYL-X 2.1

 2. Quick Introduction to SYBYL-X
Get Help

2.5 Get Help

To learn about a specific feature or dialog from within SYBYL:
• Press the keyboard F1 key.
• Press the Help button in any dialog.
• Select Help on the SYBYL menubar.
• Type HELP in the console.

The Tripos Bookshelf is SYBYL’s complete online documentation. It is

organized by SYBYL application and consists of:
• HTML-style pages that provide context-sensitive help within the
software. To ensure easy navigation, each page is linked to the table of
contents and the index of the book it belongs to as well as to the Tripos
Bookshelf’s main page. It is also equipped with a bread crumb locator.
• PDF copies of all the manuals. The “View or Print” link in each
Bookshelf topic’s main page gives you access to the complete documen-
tation for that topic in PDF format.
• A full text search engine.

To access the documentation independently of the SYBYL application:

• Linux—In the applications list: SYBYL-X n.n > Utilities > Bookshelf
• Windows—All Programs > SYBYL-X n.n > Utilities > Bookshelf
• Mac—Finder’s Go > Applications > SYBYL-X n.n Bookshelf

2.5.1 Search for Specific Information

To use the search engine click the Search tab then type the text you want to
look for in the search box and click Search or press the Enter key on your
keyboard. The list of documents found is ordered by decreasing number of
occurrences of the search text.

2.5.2 SYBYL Version and Local System Information

Help > About SYBYL

A dialog provides the following information:

• The SYBYL version, platform type, and creation date.
• The copyright notice.

SYBYL-X 2.1 SYBYL Basics 21

2. Quick Introduction to SYBYL-X
Exit SYBYL

• Your Server Host ID number. After registering to the Tripos Web site,
enter this number in your profile to gain access to the SYBYL software
download section.
• A System Info button to obtain more detailed information in the
System Messages area. This information is useful when you contact your
Tripos Support office.

2.6 Exit SYBYL

Exiting SYBYL means closing the SYBYL session. If you have multiple
sessions open simultaneously you must close each of them individually.

2.6.1 How to Exit SYBYL

Exit SYBYL in any of the following manners:

From the Menubar:

File > Exit

When exiting SYBYL via the menubar you will be prompted whether to save
molecules and spreadsheets that have not been saved after the most recent
modification.

In the Console:
Type: exit or quit.

When exiting SYBYL at the command line you will be asked to confirm the
exit.

2.6.2 End the Tutorial

! File > Exit

22 SYBYL Basics SYBYL-X 2.1

 2. Quick Introduction to SYBYL-X
Starting SYBYL-X and Setting its Environment

2.7 Starting SYBYL-X and Setting its Environment

There are several ways to access SYBYL-X. Each serves a different purpose.
You will find all access modes on the SYBYL-X 2.1 look-aside menu in your
computer’s list of programs or applications.

2.7.1 Standard SYBYL-X Startup

The easiest way to start SYBYL is via the desktop icon, , if it was placed
there during software installation.

The standard SYBYL application includes a menubar, toolbars, a graphics

window, a command console, and a system messages area. See The SYBYL
Window on page 27 for a full description.

If there is no SYBYL icon on your desktop, launch SYBYL as follows:

Windows:
• All Programs > SYBYL-X 2.1 > SYBYL-X

Linux:
• Applications menu > SYBYL-X 2.1 > SYBYL-X
• Or, in a system shell and replacing $TA_ROOT with its full path, type:
$TA_ROOT/sybyl -graphics

Mac:
• If SYBYL-X 2.1 is in your Dock double-click it.
• If SYBYL-X 2.1 was installed “for all users”: In the Finder’s Go menu
select Applications, then SYBYL-X 2.1. Double-click on SYBYL-X.
• If SYBYL-X 2.1 was installed by a single user with no administrator
privilege: In the Finder’s Go menu select Home, then bin, then
SYBYL-X 2.1. Double-click on SYBYL-X.

SYBYL-X 2.1 SYBYL Basics 23

2. Quick Introduction to SYBYL-X
Starting SYBYL-X and Setting its Environment

2.7.2 SYBYL-X Plus Console

You may start SYBYL with an additional, separate system console. Although
you may not type in this console, a small amount of information will be directed
to it by most SYBYL utilities (described in the UNITY Manual). Information in
this console may be useful for debugging purpose.

To launch SYBYL with the additional system console:

Windows:
• All Programs > SYBYL-X 2.1 > Utilities > SYBYL-X Plus
Console

Linux:
• Applications menu > SYBYL-X 2.1 > Utilities > SYBYL-X Plus
Console
• Or, in a system shell and replacing $TA_ROOT with its full path, type:
$TA_ROOT/sybyl -graphics -xterm

Mac:
• If SYBYL-X 2.1 was installed “for all users”: In the Finder’s Go menu
select Applications, then SYBYL-X 2.1. Double-click on SYBYL-X
Plus Console.
• If SYBYL-X 2.1 was installed by a single user with no administrator
privilege: In the Finder’s Go menu select Home, then bin, then
SYBYL-X 2.1. Double-click on SYBYL-X Plus Console.

2.7.3 SYBYL-X Command Line

You may start SYBYL for use of its command line operations only. In this
mode only the command console is available. The SYBYL graphics window,
menubar and toolbars are not displayed.

To launch SYBYL in command mode only, without the graphics window:

Windows:
• All Programs > SYBYL-X 2.1 > Utilities > SYBYL-X Command
Line

Linux:
• Applications menu > SYBYL-X 2.1 > Utilities > SYBYL-X
Command Line
• Or, in a system shell and replacing $TA_ROOT with its full path, type:

24 SYBYL Basics SYBYL-X 2.1

 2. Quick Introduction to SYBYL-X
Starting SYBYL-X and Setting its Environment

$TA_ROOT/sybyl -text

Mac:
• If SYBYL-X 2.1 was installed “for all users”: In the Finder’s Go menu
select Applications, then SYBYL-X 2.1. Double-click on SYBYL-X
Command Line.
• If SYBYL-X 2.1 was installed by a single user with no administrator
privilege: In the Finder’s Go menu select Home, then bin, then
SYBYL-X 2.1. Double-click on SYBYL-X Command Line.

2.7.4 SYBYL-X Environment Shell

A large number of applications that are accessible from within SYBYL may
also be run in standalone mode. Examples of these are many utilities (described
in the UNITY Manual), Surflex-Dock and Surflex-Sim, Concord, among others.
All that is required to run these applications is a system shell in which
SYBYL’s environment variables have been defined.

To open a system shell in which the SYBYL environment has been defined:

Windows:
• All Programs > SYBYL-X 2.1 > Utilities > SYBYL-X Environment
Shell

Linux:
• Applications menu > SYBYL-X 2.1 > Utilities > SYBYL-X
Environment Shell
• Or, in a system shell and replacing $TA_ROOT with its full path, type:
$TA_ROOT/sybyl -shell -xterm

Mac:
• If SYBYL-X 2.1 was installed “for all users”: In the Finder’s Go menu
select Applications, then SYBYL-X 2.1. Double-click on SYBYL-X
Environment Shell.
• If SYBYL-X 2.1 was installed by a single user with no administrator
privilege: In the Finder’s Go menu select Home, then bin, then
SYBYL-X 2.1. Double-click on SYBYL-X Environment Shell.

SYBYL-X 2.1 SYBYL Basics 25

2. Quick Introduction to SYBYL-X
Starting SYBYL-X and Setting its Environment

2.7.5 Automatic Command Execution at SYBYL Startup

You may customize the SYBYL interface for your own use by storing in a file
the SYBYL instructions to be executed every time you start the application.
This file, called sybyl.ini, must be placed in your home directory ($HOME).

Location of your HOME Directory:

• Linux and Mac platforms: HOME is the directory you are in upon
opening a terminal window.
• Windows platforms:
• Windows XP: your Documents and Settings/user folder
• Windows 7: your Users/username folder

How to Customize SYBYL:

Refer to The sybyl.ini File in the Customizing SYBYL section of the Tripos
Bookshelf for details and for a sample file.

26 SYBYL Basics SYBYL-X 2.1

 3. The SYBYL Window

When SYBYL starts its main window is presented. The graphics window
contains the menubar, toolbar icons, and the display area. The console is docked
below the display area.

All layout changes you make are preserved in .sybyl/windowState within

your home directory or folder. Different versions of this file are used by
different versions of SYBYL-X.

• The SYBYL Menubar on page 28

• SYBYL Menus
• Menu, Dialog, and Mouse Shortcuts
• The SYBYL Toolbar Icons on page 31
• The SYBYL Textports and Consoles on page 32
• Special CharactersSpecial Keyboard Keys on page 34

SYBYL-X 2.1 SYBYL Basics 27

3. The SYBYL Window
The SYBYL Menubar

3.1 The SYBYL Menubar

A SYBYL menu option can:
• execute a simple command: Edit > Delete Everything
• lead to submenus: View > Hydrogen Bonds > Intermolecular
• open a dialog: Compute > Energy...

When you initiate an operation by clicking a menu item, no other operation is

possible until either that operation has finished or until you cancel it. All
menubars are greyed out while the current operation is active.

3.1.1 SYBYL Menus

Each list of menu options can be detached from the menubar so that it remains
visible even after a selection is made.
• To detach a menu: click the dashed line above the first item.
• To close a tear-off: click the X in the upper right corner.

File Contains options to load information for display in

SYBYL or spreadsheets. It also has options for saving
files, editing text files, managing sessions, and exiting
SYBYL.
Edit Focus on creating and modifying structures in the
SYBYL display. It contains options for operations such
as clearing the screen, sketching, modifying, copying,
merging, and extracting structures.
View Options affecting the visualization of structures in the
SYBYL display. It contains options for operations such
as coloring, labeling, hiding, managing backgrounds,
surfaces, and monitors and accessing the 2D Viewer.
Tools for measuring are also found here.
Compute SYBYL’s minimization and dynamics tools can be
accessed. It contains options for calculating charges,
loading force field parameters and conformational
searches. This menu also contains options for analyzing
the results of the calculations, defining aggregates, and
defining constraints.
Applications Accessing the specialized tools and techniques offered
by Tripos for use in SYBYL. Tools for matching and
fitting are also found here.
Biopolymer Functionality specific to biopolymer structures.

28 SYBYL Basics SYBYL-X 2.1

 3. The SYBYL Window
The SYBYL Menubar

UNITY Tools for performing various types of database

searches.
Options Access to the interface for setting tailor variables. The
default molecule area and directory can be changed
from this menu and various lists and information can be
obtained. Functionality for recording and playing back
command sequences is also available.
Help Options for accessing the Tripos Bookshelf (HTML
version of the SYBYL documentation). Release notes
and other information about the current version are also
available from this menu.

See the SYBYL Menubar to Command Mapping (accessible from the Tripos
Bookshelf’s main page) to find a complete listing of options for each menu
item, with links to descriptions and corresponding commands.

3.1.2 Menu, Dialog, and Mouse Shortcuts

Menu Shortcuts

You can navigate within the SYBYL menu using the keyboard.
1. Press the keyboard Alt key while typing the underlined letter corresponding
to the menu of interest. For example, Alt+E opens the Edit menu.
2. Once a menu is open:
• Simply type the underlined letter associated with the item of interest.
• Use the keyboard arrow keys to navigate within the menu.
• Press the keyboard Enter key to activate the highlighted menu item.

Dialog Shortcuts

Within a dialog:
• Press the keyboard Tab key to skip to the next field or item in a list.
• Use the keyboard arrow keys to move up or down in a list.
• Use the mouse’s scroll wheel to select an item in a pull-down menu or to
move a slider’s position.
• In a dialog containing a single list of option, double-click an item to
select the option and close the dialog.

SYBYL-X 2.1 SYBYL Basics 29

3. The SYBYL Window
The SYBYL Menubar

Where is the dialog?

If SYBYL seems unresponsive, it may be because the active dialog has
become hidden by another window.
Click (stack windows) to bring the active window in front of the
display area.

Mouse Shortcuts

The following shortcuts involve the mouse:

• If your mouse has a scroll wheel you can use it in the graphics area to
zoom in and out. This scaling action applies to all objects, whether
visible or temporarily hidden.
• Right-click on the following objects to display relevant context menus:
• an atom
• a surface or ribbon
• the SYBYL backdrop

Use the mouse with keyboard keys to make selections and to move objects.
• Selecting With the Mouse on page 58
• Rotate, Translate, and Scale Molecules on page 17

30 SYBYL Basics SYBYL-X 2.1

 3. The SYBYL Window
The SYBYL Toolbar Icons

3.2 The SYBYL Toolbar Icons

Use the icons in the SYBYL toolbars to interact with the graphics.

A toolbar can be docked under the menubar or to either side of the display area
or it can be “torn off” so that it exists as its own window. Simply click the line
in front of a group of icons and dragging the toolbar to its new location.

To activate an icon, click it. Any dialogs that are displayed can remain open as
you work or you can close them by clicking the X in the upper corner or their
window.

Standard

Edit

View

Display

Molecule

Selection

Transformation

Biopolymer

Mouse Mode

Miscellaneous

Refer to the SYBYL Reference Guide for icon descriptions.

SYBYL-X 2.1 SYBYL Basics 31

3. The SYBYL Window
The SYBYL Textports and Consoles

3.3 The SYBYL Textports and Consoles

Three textports/consoles are docked within the main SYBYL window, initially
below the graphics window.
1. Command Console
This textport contains the interactive SYBYL prompt (SYBYL>). Type any
SYBYL command at the prompt to execute it immediately. When the
operation completes the SYBYL prompt will reappear. See the List of
SYBYL Commands in the SYBYL Reference Guide.
2. System Messages
This textport contains the text output of system operations. A few SYBYL
functions report information in this area. You may also type simple system
commands in the Command Console (e.g. type cmd ls to list the files in the
current directory or folder). The output of such a command appears in the
System Messages area.
3. Job Control Console
This console monitors jobs that have been submitted either to run in the
background on the local machine or to run remotely. Use the button to
terminate a selected process. You may also remove a process from the list
(note that this does not kill the process, only removes the item from the
displayed list), display process information, or refresh the list. Instructions
for Job Control setup can be found at https://tools.certara.com/confluence/
display/SYB/Job+Control.

3.3.1 Textport and Console Position and Visibility

The Command Console, System Messages area, and Job Control console are
initially docked side-by-side. Use the sash between them to re-apportion the
space given to each.

To detach a textport or console click its icon. To re-dock a detached

window, drag its title bar to any edge within the SYBYL graphics window.
Where and how the window re-docks is determined by the position of the
cursor.

To hide a textport or console click its X button. To display it again use the
appropriate View > Console Display menu item (or the CONSOLE command).

3.3.2 Textport Font

To adjust the font size and type right-click in the Command Console and select
Change Console Font. Your new selection will be used in the current and
subsequent SYBYL sessions.

32 SYBYL Basics SYBYL-X 2.1

 3. The SYBYL Window
The SYBYL Textports and Consoles

3.3.3 Typing Commands in the Console

Although most SYBYL functions are available via the menubar and toolbars,
you may need or prefer to type some SYBYL commands in the Command
Console.

You may enter a command and all its options on a single line. Only the shortest
unique string needs to be typed to identify a command or any of its arguments.

If you type only the command name then press Enter, you will be prompted for
the necessary arguments with default values in angle brackets.

SYBYL has two modes for command operations:

• In the standard mode, commands are entered in the console but object
selections can also be done via the “expression” dialogs. Pressing the
Enter key after each argument will display the appropriate dialog when
an object selection is required.
• You may also switch to a mode in which once a command name has
been typed its remaining arguments must be entered in the console

To activate command-only mode type: SET PICKING NO_PICKING

To return to the standard mode, type: SET PICKING OBJECT_ONLY

3.3.4 Special Characters

When interacting with SYBYL in the Command Console use the following
characters:
• ?—Use the help character at any time to obtain information about a
command, the values of an argument, or the format of a specific
parameter.
• ^ (caret)—Use the abort character in response to any prompt to
terminate the command operation. No changes are made to the
molecule(s).
• | (vertical bar)—Use the end loop character to terminate the entry of
parameters being requested in an indefinitely repeating loop. When you
have completed all the required entries, respond to the next prompt with
the end loop character. SYBYL terminates the request loop and executes
the command or moves on to the next parameter.
• Ctrl-Y—Terminate the execution of a SYBYL command or SPL script
on Linux platforms.

SYBYL-X 2.1 SYBYL Basics 33

3. The SYBYL Window
Special Keyboard Keys

3.4 Special Keyboard Keys

Key Action
F1 Help
F7 Toggle hardware stereo on and off. F7 is active only if
the necessary hardware is available. See Hardware Ste-
reo in the Installation and Administration Manual.
F9 Toggle mouse focus between Global and D1.
F10 Toggle between Global and D2.
F11 Toggle between Global and D3.
F12 Toggle between Global and D4.
Ctrl + Up arrow Rotate all displayed objects +90° about the X-axis.
Ctrl + Down arrow Rotate all displayed objects –90° about the X-axis.
Ctrl + Left arrow Rotate all displayed objects +90° about the Y-axis.
Ctrl + Right arrow Rotate all displayed objects –90° about the Y-axis.

Mac Users
By default keys F9–F12 are assigned to other operations. To configure them for
use in SYBYL: System Preferences > Keyboard > Keyboard Shortcuts. You
will find F12 under Dashboard & Dock and F9, F10, F11 under Exposé &
Spaces.

To rotate by 90° use the Command key and the keyboard arrows.

34 SYBYL Basics SYBYL-X 2.1

 4. Read and Write Files of Molecules
• Import (Read) Molecules From Files on page 36
• Export (Write) Molecules to Files on page 40
• Molecule File Formats on page 42
• Mol2 Files on page 42
• SLN Files on page 43
• MDL SD and Mol Files on page 43
• Benchware 3D Explorer Files on page 46
• Convert Between Molecular File Formats on page 49

See Also:
Image: Save to File, Copy to Clipboard in the Graphics Manual

SYBYL-X 2.1 SYBYL Basics 35

4. Read and Write Files of Molecules
Import (Read) Molecules From Files

4.1 Import (Read) Molecules From Files

SYBYL’s file browser presents slight differences depending on context:
• Open a file to import it into SYBYL: File > Import File ( ). A
molecule area is often associated with that operation.
• Open a SYBYL session: File > Open Session ( ). Each saved
SYBYL session consists of many files stored in a directory with the .ses
extension.
• Save an image to a file: File > Save Image.
• Save a spreadsheet to a table (.tbl) file: MDE: File > Save As.

Common Features

Directory The full path to the currently selected directory. The

pull-down provides access to the parent directories.

36 SYBYL Basics SYBYL-X 2.1

 4. Read and Write Files of Molecules
Import (Read) Molecules From Files

Toolbar
• —Go back to the previously selected directory
or folder.
• —Go up one level in the directory tree, that is,
the parent directory.
• —Delete the file(s) selected in the list.
• —Create a new directory or folder within the
currently selected directory. This button is disabled
if you do not have permission to write to the
selected directory (e.g. the SYBYL demo
directory).
Bookmarks Provide quick access to commonly used directories. By
default, the current working directory (identified by the
variable $CWD), your home directory (identified as
$HOME), and SYBYL’s demo directory (set by the
variable $TA_DEMO) are listed. If you change direc-
tory while in SYBYL, the variable $CWD is updated to
reflect the change.
• To add another directory to the list, navigate to that
directory then press the button.
• To remove a directory from the list, click that
directory and press the button. (Note that the
default bookmarks cannot be removed.)
User-defined bookmarks are stored and can be directly
edited in your “home directory”/.sybyl/
directory_bookmarks file.
Directory Navi- Select one of the sub-directories if you want to select a
gation file from it.
Note: Use the vertical sash to the right of this list to
widen this section of the dialog.
Selection List all files of the specified format in the selected
directory. Double-click a single file to open it or hold
the Ctrl key (Command on the Mac) while selecting
multiple files to open them all.
The list can be sorted by file name or modification date.

On File > Import File

File to Read The name(s) of file(s) selected to be read in. You may
type a subdirectory name or a full directory path and
press OK to list the files it contains. You may also type
the name of a file.
The field label depends on how the dialog was invoked.

SYBYL-X 2.1 SYBYL Basics 37

4. Read and Write Files of Molecules
Import (Read) Molecules From Files

Files of Type Options depend on how this dialog was invoked.

• Molecule—Lists files containing molecules (e.g.,
.mol2, .pdb, .sln, .hits, . sdf, …). Selected file(s)
will be loaded into molecule areas. Files of type
SLN and SD are loaded into spreadsheets. If a Mol2
file contains multiple molecules, you will be given
the choice to load the contents into a spreadsheet or
separate molecule areas.
• SYBYL Mol2—Lists files with the .mol2
extension. Selected file(s) will be loaded into
molecule areas. If a file contains multiple
molecules, you will be given the choice to load the
contents into a spreadsheet or separate molecule
areas.
• SLN—Lists files with the .sln, .hits and .chom
(Legion) extensions. Selected file(s) will be loaded
into spreadsheets, one for each file.
• MDL-SDF—Lists only MDL .sdf files, a data
format that can contain multiple chemical structures
and arbitrary data associated with those structures.
The selected file(s) will be loaded into spreadsheets,
one for each file.
• SMILES—Lists structure files in SMILES format
with .smi and .smiles extensions. The selected
file(s) will be loaded into spreadsheets, one for each
file.
• PDB—Lists files containing proteins (e.g., .pdb,
.ent, …). The selected file(s) will be loaded into
molecule areas.
• Sequence—Lists files containing sequences (e.g.,
.pir, .fast). The selected file(s) will be loaded into
molecule areas and into the Sequence Viewer.
• Spreadsheet—Lists files that can be loaded into a
spreadsheet (e.g., .tbl, .hits, .sln, .3db, .sdf, and
.chom (created by Legion)). The selected file(s)
will be loaded into spreadsheets, one for each file.
• Delimited File—Lists text files in delimited format
(.csv, .tsv, .txt). The selected file(s) will be loaded
into spreadsheets, one for each file.
• Database—Lists database files in SYBYL (.mdb)
and UNITY (.tdb) formats. The selected file(s) will
be loaded into spreadsheets, one for each file.
• 3D Explorer—Lists .b3d files. The selected file(s)
will be loaded into molecule areas. Refer to
Benchware 3D Explorer Files on page 46.
• Any File—Lists all entries in the directory.

38 SYBYL Basics SYBYL-X 2.1

 4. Read and Write Files of Molecules
Import (Read) Molecules From Files

Molecular Areas When appropriate, list of molecule areas and names of

any currently displayed structures. By default, SYBYL
automatically selects the first available molecule area.
If multiple files are selected, molecules are loaded in
consecutive molecule areas.

On File > Open Session

See Manage SYBYL Sessions on page 195 for additional information.

Directory Name of the session directory selected at the top of the

dialog.
Files of Type Session (*.ses)

On File > Save Image

See Image: Save to File, Copy to Clipboard (in the Graphics Manual) for
additional information.

Filename Enter the name of the file to be created.

Files of Type • JPEG File (*.jpg *.jpeg)
• Bitmap File (*.bmp)
• PNG File (*.png)
• TIFF File (*.tif *.tiff)
Image Dimen- The Width and Height of the image as captured are
sions reported in Inches and Pixels for the specified DPI
value (default is 300). You may modify these before
saving the image to a file. Note that these values are
interdependent and that the proportions will be main-
tained. After modifying a value, press the Enter key to
effect the change.
JPEG Options The Quality Slider provides an image compression
mechanism.

Additional Information:
• Load Molecules on page 16 for an example exercise
• Export (Write) Molecules to Files on page 40
• Molecule File Formats on page 42

SYBYL-X 2.1 SYBYL Basics 39

4. Read and Write Files of Molecules
Export (Write) Molecules to Files

4.2 Export (Write) Molecules to Files

Use the File > Export File ( ) option to save one or more molecules. By
default, SYBYL saves the selected molecule(s) in the specified format to the
current working directory. What is saved with the file depends on the file type.

Only the selected molecules are saved, not associated background images, if
any are present.

! File > Export File ( )

File Name for the file being saved. You can accept the default,
enter a new file name, or specify a different directory via
the [...] button.
Acceptable file names:
• 3 to 15 alphanumeric characters
• May include _ (underscore) or a - (hyphen)
• May not include spaces or other special characters
The file extension is provided automatically to match the
selected format.
Format Select the file format.
Note: You can save multiple structures in a single file in
Mol2 or MDL-SDF format.
Molecule List Use the buttons (Select All, Invert, and Clear) to select
the molecule(s) to save. The dialog reports the total number
of selected molecules and the total number of molecules in
the list.

Additional Information:
• Save a Molecule to a File on page 20 for an example exercise
• Mol2 Files on page 42
• Molecule File Formats on page 42

40 SYBYL Basics SYBYL-X 2.1

 4. Read and Write Files of Molecules
Export (Write) Molecules to Files

• Read and Write PIR and FASTA Files in the Biopolymer Manual
• Read and Write PDB Files in the Biopolymer Manual
• Tailor subject PDB in the Tailor Manual
• SLN Files on page 43
• MDL SD and Mol Files on page 43

SYBYL-X 2.1 SYBYL Basics 41

4. Read and Write Files of Molecules
Molecule File Formats

4.3 Molecule File Formats

4.3.1 Mol2 Files
SYBYL uses Mol2 files (.mol2) to store molecules resulting from most compu-
tations.

A Mol2 file is a text file containing all information necessary to reconstruct one
or more molecule(s). The format is based upon the convention of a keyword for
each type of data, followed by a group of records. For details refer to the Mol2
File Format (see https://tools.certara.com/confluence/display/SYB/
Mol2+File+Format).

Read and Write Via the Menubar and Toolbar

Read: File > Import File ( ) with File Type set to SYBYL Mol2.
The selected file(s) will be loaded into molecule area(s). If a file
contains multiple molecules, you may choose to load the con-
tents into a spreadsheet or separate molecule areas.
Write: File > Export File ( ) with Format set to Mol2.
The selected molecule(s) are written to a single .mol2 file.

Read and Write Via the Command Console

MOL direction [mol_area] filename

Direction: • DIRECTORY—Report if the specified file has Mol2 format.

For each molecule in the file, list the molecule name and the
number of atoms and bonds.
• IN—Read a file containing a single molecule.
• MULT_IN—Read a file containing several molecules, starting
at the specified area and filling subsequent areas thereafter,
until all molecules are read.
• OUT—Write a file containing a single molecule in the
specified area.
• MULT_OUT—Write a file containing several molecules in
several molecule areas.
mol_area: Molecule area to receive input data (IN, MULT_IN) or that con-
tains molecule(s) to write to a file (OUT, MULT_OUT). Contents of
the specified molecule areas are overwritten.

42 SYBYL Basics SYBYL-X 2.1

 4. Read and Write Files of Molecules
Molecule File Formats

filename: Name of the file to read or write. When writing a file, if the file-
name already exists, it is overwritten.
Note: Only one file can be handled at a time. To read multiple
files you must issue the command for each separate files.

Default Names for Unnamed Molecules

All molecules stored in a Mol2 file must have a name. This name is usually
provided by the context of the operation or via Edit > Molecule > Name.

The Tailor variable MOL AUTO_NAME determines how to handle unnamed

molecules during import into SYBYL:
• YES: unnamed molecules (in single and multi-Mol2) are named
according to the filename.
• NO: unnamed molecules are named “unnamed”.

4.3.2 SLN Files

SLN files are structure files with .sln, .hits or .chom (Legion) extensions. Files
in SLN format can contain multiple chemical structures and arbitrary data
associated with those structures.

A file of type SLN must start with the line:

#SYBYL/3DB HITLIST

Read: File > Import File ( ) with File Type set to SLN.
The contents of the selected file(s) are loaded into spread-
sheet(s), one for each file.
Write: File > Export File ( ) with Format set to SLN.

Refer to the SLN Manual for a complete description of the SLN format.

4.3.3 MDL SD and Mol Files

Files in MDL SD format can contain multiple chemical structures and arbitrary
data associated with those structures.

SYBYL-X 2.1 SYBYL Basics 43

4. Read and Write Files of Molecules
Molecule File Formats

Read and Write Via the Menubar and Toolbar

Read: File > Import File ( ) with File Type set to MDL-SDF.
The selected MDL Mol file(s) will be loaded into molecule
area(s). The contents of MDL SD file(s) are loaded into spread-
sheets, one for each SD file.
Note: Normalization (aromatization and standardization) of the
structures is done by default. To control this behavior, use
Options > Tailor > TABLE and modify
MDL_NORM_AROM.
Write: File > Export File ( ) with Format set to MDL-SDF.
The selected molecule(s) are written to a single .sdf file.
Note: To include hydrogens when saving to an SD or MDL Mol
file, use Options > Tailor > TABLE and set
MDL_H_HANDLING to KEEP_ALL.

Read and Write Via the Command Console

MDLMOL direction mol_area filename(s)

Direction: • IN—Read an MDL Mol file. Assign correct atom and bond
types (verify that they are correct before proceeding). Non-
recognized atoms are assigned SYBYL’s type DU (dummy).
Files with more than 999 atoms or bonds cannot be read.
Note that normalization (aromatization and standardization)
of the structures is done by default. To control this default
behavior, use the Tailor variable TABLE MDL_NORM_AROM.
• OUT—Write a MDL Mol file. Use the molecule’s name as the
file header name, and prompt for the header and comment
line. SYBYL aromatic bonds are converted to alternating
single and double bonds. SYBYL dummy atoms (DU) and
lone pairs (LP) are removed from the atom list before the file
is written.
• MULT_IN—Read the contents of an SD file into molecule
areas.
• MULT_OUT—Save multiple molecules to an SD file.
mol_area: Molecule area to receive input data (IN, MULT_IN) or that con-
tains molecule(s) to write to a file (OUT, MULT_OUT). Contents of
the specified molecule areas are overwritten upon import.
filename: Name of the file to read or write. When writing a file, if the file-
name already exists, it is overwritten.

Notes:

44 SYBYL Basics SYBYL-X 2.1

 4. Read and Write Files of Molecules
Molecule File Formats

• When reading MDL SD or Mol files, normalization (aromatization and

standardization) of the structures is done by default. To control this
default behavior, use the Tailor variable TABLE MDL_NORM_AROM.
• To include hydrogens when saving to an SD or MDL Mol file, use the
Tailor variable TABLE MDL_H_HANDLING to KEEP_ALL.

SYBYL-X 2.1 SYBYL Basics 45

4. Read and Write Files of Molecules
Molecule File Formats

Convert MDL SD File to Other Formats

MDLMOL_CONVERT output_format input_file name_field

output_name
• output_format—HITLIST (file in SLN format) or MSS (spreadsheet .tbl
file)
• input_file—Name of MDL SD file to convert.
• name_field—Registration/Name field to look for in the MDL SD file
(case sensitive).
• output_name—Name to assign to the generated SLN file or spreadsheet.

The same operations may be performed as follows:

• File > Import File ( )
• File of Type: MDL-SDF
• The file is automatically loaded into a spreadsheet.
• File > Translate Molecular File
• Input File Type: MDL-SDF
• Output File Type: SLN (or any other format)

4.3.4 Benchware 3D Explorer Files

SYBYL-X can read and write structure files in Benchware 3D Explorer format
to support easy transfer of information between the two software products.

Platform Note: This functionality is not available on the Mac.

Read and Write Via the Menubar and Toolbar

Read:
File > Import File ( ) with File Type set to 3D Explorer.
The selected .b3d file(s) will be loaded into molecule area(s).
Usage Note: You must close the file in Benchware 3D Explorer
before attempting to import it into SYBYL.
Write: File > Export File ( ) with Format set to 3DE.
The selected molecule(s) and associated surfaces are written to a
single .p3d file.

46 SYBYL Basics SYBYL-X 2.1

 4. Read and Write Files of Molecules
Molecule File Formats

Supported in SYBYL-X

Feature SYBYL to 3D Explorer 3D Explorer to SYBYL

Molecule X X
Name X X
Coloring X
Rendering style X X
Type: ligand vs. X
protein
Scale X
Orientation X X
Relative X
translation
Surface X X
Coloring X X
Ribbons X X
Rendering style X X
Atom association X
Scale X
Orientation X X

How to Update Benchware 3D Explorer to Match Surface Traits in SYBYL-X

SYBYL-X colors protein surfaces by properties that are not defined in
Benchware 3D Explorer. There properties are packing density, hydrogen bond
acceptor/donor density, cavity depth, and secondary structure.

This may be remedied easily by copying the file containing the property color
ranges from your SYBYL-X installation to your Benchware 3D Explorer instal-
lation, overwriting the existing file.

The following file paths are provided assuming that both products were
installed in the default locations:
• From SYBYL-X 1.2 or more recent:
On Windows: C:\tripos\sybylx1.2\tables\trait_colors
On Linux: $TA_ROOT/tables/trait_colors

SYBYL-X 2.1 SYBYL Basics 47

4. Read and Write Files of Molecules
Molecule File Formats

• To Benchware 3D Explorer:
C:\Program Files\Tripos\Benchware\3D Explorer\tables\trait_colors

Questions and Answers

Why are surfaces colored by atom color different in SYBYL-X and Benchware
3D Explorer?
Because SYBYL-X and Benchware 3D Explorer use different algorithms to
determine atom proximity to a surface point, surfaces colored by atom color
(not atom type) may appear slightly different in both applications.

48 SYBYL Basics SYBYL-X 2.1

 4. Read and Write Files of Molecules
Convert Between Molecular File Formats

4.4 Convert Between Molecular File Formats

Convert molecular descriptions from one file format to another, performing
some additional operations during the conversion process.

For the expert: utilities described in the UNITY Manual

• dbtranslate: Translate between Molecule Formats
• sln2img: Translate SLN or SMILES Files to PNG or GIF

UNITY > UNITY Tools > Translate Molecular Files

or

File > Translate Molecular Files

Input Options

Enter SLN The SLN string for the input structure.

Mol Area The molecule area containing the input structure.
File The type of the input file: SLN, BCD (BinConf) (binary
conformational data file), MDL-SDF, Original
SMILES, Daylight SMILES, Conversational
SMILES, SYBYL MOL2. Enter the file’s full path or
press [...] to access a file browser.
(Read about Binary Conformational Data Files in the
UNITY Manual.)

SYBYL-X 2.1 SYBYL Basics 49

4. Read and Write Files of Molecules
Convert Between Molecular File Formats

Output Options

SLN to Textport Print the output SLN in the command console.

Mol Area Select the molecule area to receive the first output struc-
ture. Note: Molecules placed in SYBYL molecule areas
do not retain any property data.
File Type Save results to a file of the specified type: SLN, BCD
(BinConf) (binary conformational data file), MDL-SDF,
Original SMILES, Daylight SMILES, Conversa-
tional SMILES, SYBYL MOL2, SLN Tabs (gives
regID, a tab, then SLN.) If the input is BCD, the regIDs
and number of conformations are provided in the output
file. Enter the file’s full path in the Name field or click
[...] to browse to the desired location. A file extension is
automatically added to reflect the selected file type.
For BCD (BinConf), if the specified file exists, infor-
mation will be appended to it (i.e., the contents will not
be overwritten). Read about Binary Conformational Data
Files in the UNITY Manual.
Specify Options Display the Translate Molecular File Options dialog for
further translation choices.

4.4.1 Specify Translation Options

UNITY > UNITY Tools > Translate Molecular Files
In the Translate Molecular File dialog, press Specify Options.

50 SYBYL Basics SYBYL-X 2.1

 4. Read and Write Files of Molecules
Convert Between Molecular File Formats

Generate Concord 3D Use Concord to generate 3D coordinates. (Read

Coordinates about the use of Concord for this operation in the
UNITY Manual.) Enter the number of structures
to give to Concord per batch in the Batch Size
field. Default is 500.
Perceive Chirality at Check for the chirality of carbon atoms based on
Carbons 3D coordinates or, if coordinates are not present,
bond stereo flags. Existing chirality attributes
that perception determines are incorrect, will be
removed. (Not recommended for 2D SD files.)
Perceive Chirality at N Set chirality for nitrogen and phosphorus atoms
and P based on 3D coordinates or, if coordinates are
not present, bond stereo flags. Existing chirality
attributes that perception determines are incor-
rect, will be removed. (Not recommended for 2D
SD files.)

SYBYL-X 2.1 SYBYL Basics 51

4. Read and Write Files of Molecules
Convert Between Molecular File Formats

Perceive Bond Stere- Set double bond stereo based on 3D coordinates

ochemistry or, if coordinates are not present, bond stereo
flags. Use the environment variable
PERCEIVE_RING_BONDS to control how stereo
bond attributes are perceived in rings. Existing
stereo attributes that perception determines are
incorrect, will be removed. (Not recommended
for 2D SD files.)
Include/Strip Property Turn on to include property data.
Data
Standardize Structures Check to enable standardization of structures by
using rules defined in standard.defs (by
default). (Read about Standardizing Structures in
the UNITY Manual.)
Standardization Rules Specify a different file to use for standardization
File rules.
Output for SYBYL Force output to be “SYBYL friendly.” Only six
Compatibility membered rings are aromatized, and charge sep-
arated nitro groups are converted to N(=O)=O.
Two files residing in the UNITY database direc-
tory (path set by TA_FILE_PATH) are used,
mol2_arom.defs (special version aromatic-
ity.defs), and mol2_standard.defs (special
version of standard.defs).
Fill Valences Fill valences of translated structure.
Aromatize Structures Automatically perform aromatic normalization.
Convert to Kekule Use the Kekulé bonding scheme. Available only
if Aromatize Structures is off.
Validate Valences • Off—Prevent validation of structures.
• Warning—Validate structures, but do not
write invalid structures to a file.
• Error—Validate structures and save invalid
structures to designated file.
Invalid Structures File File to hold invalid structures. Only valid if Vali-
date is set to Error.
Treatment of H’s in How to handle hydrogens. Only valid when out-
MDL-SD Files put type is SD File.
• chiral_only—Keep hydrogens located on
chiral atoms (default and MDL compatible).
• remove_all—Remove all hydrogens.
• keep_all—Keep all hydrogens.
• carbon_remove—Remove all hydrogens
located on carbons.

52 SYBYL Basics SYBYL-X 2.1

 4. Read and Write Files of Molecules
Convert Between Molecular File Formats

MDL-SDF Field to use Data label within a MDL SD file identifying reg-
for Regid istration name. Only valid when input file type is
SD File.
Expand Macro Atoms Replace macro atoms with constituent atoms,
essentially exploding them.
Unique Structures Canonicalize translated structure.
Split SLNs over Multi- Turn off to generate a single line SLN. Only
ple Lines valid when output file type is SLN.
Fast Translation Use with Split SLNs over Multiple Lines to
convert SLN files to/from multi-line SLN output.
Header information is preserved or created if not
present.
Include/Strip Atom Turn on to include chirality.
Chirality
Include/Strip Stereo When off, stereo bond attributes are stripped.
Bonds Attrs Removal of stereo bond attributes occurs prior to
stereo bond perception, when Perceive Bond
Stereochemistry is on.
Include/Strip 2D Coor- Turn on to include 2D coordinates.
dinates
Include/Strip 3D Coor- Turn on to include 3D coordinates.
dinates
Visual Report of Display progress information on host terminal.
Progress
Report_Interval Number of structures to translate before report-
ing progress information. This option has no
effect unless Visual Report of Progress is on.
Enable/Disable Debug Turn on to display debugging messages.
Mode
Write Errors to Log Name of log file to hold errors. Default is
File dbtranslate.log. Existing file is overwritten.

Remarks:
When converting between the SLN and SD formats consult the following
documents:
• Extensions to SLN for representing relative stereochemistry and
isomeric mixtures
• http://accelrys.com/products/pdf/enhanced-stereochemical-represen-
tation.pdf
The file $TA_ROOT/tables/mts_pref.defs describes how to set various
preferences that can be used when translating files in SD format.

SYBYL-X 2.1 SYBYL Basics 53

4. Read and Write Files of Molecules
Convert Between Molecular File Formats

54 SYBYL Basics SYBYL-X 2.1

 5. Understand Molecule and Display Areas

What are Molecule and Display Areas?

A display area is where your molecule is displayed on the screen. SYBYL has
four unique display areas: D1, D2, D3, and D4.

Click the icon and select from the pull-down or click the icon to open
the Display Options dialog and use the Screen options to change the placement
on the screen. The figure below shows how molecules are displayed for each
screen layout.

Figure 1 Screen Modes

A molecule area is a region of memory that holds a particular molecule. The

total number of molecule areas does not have a fixed limit, because the number
depends on your computer’s memory.

Note that molecule areas have rules:

• M1 is always in display area D1.
• M2 is always in display area D2.
• M3 is always in display area D3.
• M4 is always in display area D4.

If you use additional molecule areas, they recycle through the display areas:
• M5 is always in display area D1.
• M6 is always in display area D2.
• M7 is always in display area D3.
• M8 is always in display area D4.

SYBYL-X 2.1 SYBYL Basics 55

5. Understand Molecule and Display Areas

The figure below demonstrates this pattern.

Figure 2 Distribution of Molecule Areas in Display Areas

Additional Information:
• Load Molecules on page 16 for an example exercise
• Change the Display on page 16 for an example exercise

Change the Default Molecule Area

The default molecule area when you start SYBYL is M1.

Tip: If you are performing a number of operations on a structure in a different

area (for example, M3), you can change the default to that area (M3), while
working on that structure.

Menubar: Options > Set > Default Molecule Area

Command: DEFAULT mol_area

The default molecule area is reported in the status bar at the bottom of the
SYBYL window.

56 SYBYL Basics SYBYL-X 2.1

 6. Select Atoms, Bonds, or Substructures
• Selecting With the Mouse on page 58
• The Selection Menu and Icons on page 59
• General Description of the Expression Dialogs on page 64
• Tutorials:
• How to Use the Atom Expression Dialog on page 72
• How to Use the Bond Expression dialog on page 79
• How to Use the Substructure Expression Dialog on page 82

Selection of atoms, bonds, or substructures (such as residues in a protein) can be

as simple as clicking on the desired objects in the SYBYL display area. More
complex selection may be based on a particular type or a defined set, and may
use Boolean operations.

Many menubar and toolbar operations in SYBYL will operate on the current
selection in the display area. For example, selecting several atoms in the display
area and then clicking immediately changes the rendering of the selected
atoms (and connecting bonds) to be capped sticks.

Additional Information in the SPL Manual:

• Formats for Specifying Objects
• Create Complex Expressions

SYBYL-X 2.1 SYBYL Basics 57

6. Select Atoms, Bonds, or Substructures
Selecting With the Mouse

6.1 Selecting With the Mouse

One-click selection
• Click on an atom to select it. If the atom is spacefilled you must click in
the center of the sphere to select the atom.
• Click on a surface or ribbon to select it.

Select a residue or substructure

• Double-click on any atom in a residue to select the entire substructure.

Select an entire molecule

• Triple-click on any atom to select everything in the molecule area. In the
context of a biopolymer complex, this means the biopolymer itself as
well as any ligand, cofactor, metal and waters in the same molecule area.

Select all atoms in a rectangular area

• Ctrl+Alt while dragging the mouse to select all atoms in the area
outlined by a rectangle.
• Mac Users: Command+Alt while dragging the mouse to outline the
selection rectangle.

Toggle the selection state of an object

• Ctrl+click an atom or surface to add it to or remove it from the current
selection.
• Ctrl+double-click any atom to toggle the selection station of its
substructure.
• Ctrl+triple-click any atom to toggle the selection state of the entire
molecule area.
• Mac Users: Use the Command key with single, double or triple click.

Clear all selection

• Click anywhere on the SYBYL backdrop.
• Click .

Usage Note About Invisible Hydrogens

Invisible hydrogens connected to selected heavy atoms are selected
implicitly and are affected by operations applied to the selection.

58 SYBYL Basics SYBYL-X 2.1

 6. Select Atoms, Bonds, or Substructures
The Selection Menu and Icons

6.2 The Selection Menu and Icons

On the SYBYL menubar: Selection

Usage Notes About Invisible Atoms

• Atoms that are invisible cannot be selected and, therefore, are not acted
upon unless the operation affects the entire molecule area.
• Exception is made for invisible hydrogens connected to selected heavy
atoms. These hydrogens are selected implicitly and are affected by
operations applied to the selection.

6.2.1 Expand the Selection

This functionality is enabled only if at least one atom has been selected.

Access:
• Menubar: Selection > Expand
• Icon:
• Right-click a selected atom > Expand Selection

To Anything The selection expands to include all atoms contiguously

Connected connected to the pre-selected atom(s).
For example, in a protein/ligand complex with a ligand
atom selected, expansion selects all atoms in that ligand
and none of the protein atoms nor any atoms in addi-
tional structures such as water, metal or other ligands.

SYBYL-X 2.1 SYBYL Basics 59

6. Select Atoms, Bonds, or Substructures
The Selection Menu and Icons

To Substructure The selection expands to include all atoms in the sub-

structure(s) that contain pre-selected atom(s).
For example, in a protein with atoms selected in two
residues, expansion selects all atoms in those residues.
To Chain The selection expands to include all atoms in the pro-
tein chain(s) that contain pre-selected atom(s).
To Biopolymer The selection expands to include all biopolymer atoms
in the molecule area(s) that contain pre-selected
atom(s). Biopolymer atoms are those that fall in the
Residues listing of the Atom Expression dialog.
Examples given a solvated protein/ligand complex:
• If one protein atom is selected, expansion selects
the entire protein, but not ligand, solvent, or any
other non-protein atoms.
• If any non-residue atom is selected, expansion adds
all protein residues to the selection.
To Structure The selection expands to include all atoms in all the
molecule areas that contain pre-selected atoms.
Within a Radius The selection expands to include atoms in all molecule
areas that are within the specified radius of pre-selected
atoms.
• For small molecules the expansion selects atoms
within the specified radius.
• For biopolymers the expansion includes all
substructures that have any atom within the
specified radius.

6.2.2 Invert the Selection

This functionality is enabled only if at least one atom has been selected.

Access:
• Menubar: Selection > Invert
• Icon:

Within Selected The atom selection is inverted, but only within the mol-
Molecule Areas ecule area(s) that contain selected atom(s).
Over All Mole- The atom selection is inverted over all molecule areas.
cule Areas For example, with two molecule areas occupied and
only a single atom selected, inverting the selection over
all areas selects all atoms in both molecule areas and
deselects the atom that was originally selected.

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 6. Select Atoms, Bonds, or Substructures
The Selection Menu and Icons

Of Molecule Inversion of the selection depends on the original selec-

Areas tion:
• For molecule areas that contain selected atom(s), all
atoms will be deselected.
• For molecule areas that do not contain selected
atom(s), all atoms will be selected.

6.2.3 Clear the Selection

Clear the selection from all objects. This feature is available only if at least one
object has been selected.

Access:
• Mouse: click the left button in an unoccupied area of the SYBYL
backdrop.
• Menubar: Selection > Clear
• Icon:

6.2.4 Select All or Specified Atoms

All Atoms
Select all atoms in all molecule areas.

Access:
• Menubar: Selection > All Atoms

Some Atoms in a Single Molecule Area

Launch the Atom Expression dialog. If multiple molecule areas are occupied
select the one of interest at the top of the dialog. Only the atoms selected in the
dialog will be selected when the dialog is closed via its OK button. Invisible
hydrogens connected to the selected atoms are selected implicitly.

Access:
• Menubar: Selection > Select Atoms
• Icon:

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6. Select Atoms, Bonds, or Substructures
The Selection Menu and Icons

All Atoms in Specified Molecule Area(s)

Select all atoms in the molecule areas selected via the Molecule Expression
dialog. If only one molecule area is occupied all atoms within it are selected
automatically.

Access:
• Menubar: Selection > Select Molecules

6.2.5 Select Atoms in Biopolymers

The following options of the Selection menu make use of sets and the
macromol dictionary to select atoms in all molecule areas that contain
molecules of type “biopolymer” (protein, DNA, RNA, carbohydrate).

Biopolymer Use the {BIOPOLYMER} built-in set to select all

amino acids and nucleic acids.
Backbone Use the {BACKBONE} built-in set to select all back-
bone atoms in all molecule areas.
Sidechain Use the {SIDECHAIN} built-in set to select all
sidechain atoms in all molecule areas.
Ligand Use the {BIOPOLYMER(LIGAND} set to identify all
ligand atoms.
Note that ligand atoms in a molecule area that does not
contain any residues may also be identified by selec-
tion, show, and hide operations. This is because copy-
ing or extracting a ligand from, for example, a protein/
ligand complex into a new molecule area assigns the
type “biopolymer” to the new molecule.
Water Use the {WATER} set to select all water atoms in all
molecule areas.
Metal Use the {METAL} built-in set to select all metal atoms
in all molecule areas.

Usage Notes About Invisible Atoms

• Atoms that are invisible cannot be selected and, therefore, cannot be
acted upon unless the operation affects the entire molecule area. For
example, if only the protein and water atoms within a 5 Å radius of a
ligand are currently visible, the Selection > Water operation will select
only the visible waters, not all of them. A subsequent deletion of the
selected atoms will delete only those few visible waters, leaving all other
waters invisible, but still present.
• Invisible hydrogens connected to selected heavy atoms are selected
implicitly and are affected by operations applied to the selection.

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 6. Select Atoms, Bonds, or Substructures
The Selection Menu and Icons

6.2.6 Select Hydrogens

The following options of the Selection menu use hydrogens as the basis for
selecting atoms in all molecule areas.

Non-Hydrogens Select the visible non-hydrogen atoms in all molecule

areas.
Hydrogens Select the visible hydrogens in all molecule areas.
Polar Hydrogens Use the {POSSIBLE_HBOND} built-in set to select
among the visible hydrogens in all molecule areas.
Non-Polar Select the non-polar hydrogens that are visible in all
Hydrogens molecule areas.

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6. Select Atoms, Bonds, or Substructures
General Description of the Expression Dialogs

6.3 General Description of the Expression Dialogs

SYBYL’s Expression dialogs are designed to allow as much flexibility as
possible.

6.3.1 The Main Expression Dialog

Access:
• Menubar: Selection > Select Atoms
• Icon:
• Required selection in the context of an operation in progress.

As selections are made by clicking on The expression itself shows the mole-
objects in SYBYL’s display area or cule area and current “formula” that the
using the various buttons, an expression program will use to select the objects for
is formed. Activating the Show Atom the action being performed. As you
Expression check box will expand the become familiar with expressions, you
dialog so that the expression is visible. may enter them directly in the field. Note
that no atoms will be highlighted until
you press Apply.

The Expression dialog is presented under several different titles depending on

context: Atom Expression, Bond Expression, Substructure Expression, Sequence
Expression. Although the various Expression dialogs are very similar in layout,
there are differences. These differences are noted in the description below.

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 6. Select Atoms, Bonds, or Substructures
General Description of the Expression Dialogs

Molecule Area In the pull-down select the molecule area in which the
selection will be made.
Usage Notes:
• Picking from the screen is enabled only in this
designated molecule area.
• When the dialog is invoked via the icon
(Selection > Select Atoms), the molecule area is
set automatically to that of a pre-selected atom or, if
nothing had been selected, to the current default
molecule area as reported at the bottom of the
SYBYL window (set via Options > Set > Default
Molecule Area).
Hierarchy Contains a hierarchical representation of the structural
contents in the specified molecule area.
• When applicable, the different levels can be
expanded and collapsed by clicking the “+” and “-”,
respectively.
• Click an item in the hierarchy to select it (a check
mark appears in the check box). Atoms that are
hidden cannot be selected unless the dialog is
posted by a “Show More” operation. An exception
is made for invisible hydrogens, which are selected
implicitly with the atoms they are connected to.
• When an item with subitems is selected, all its
subitems are also selected.
• When one or more subitems are selected, the check
box of the main item will contain a grey check mark
to indicate a partial selection.
• Right-click menus are available with options for
inverting the current selection. For proteins, the
menu options allow for various degrees of inversion
(e.g., invert the selection within the substructure,
within the chain, or the entire protein).
• If a protein has missing residues within a chain, you
will see multiple entries for that chain, one for each
continuous chain of residues. The residue number
range for each portion of the chain is shown in
parentheses.
Buttons to assist in selecting items in the hierarchy:
select all, invert selection, clear selection.

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6. Select Atoms, Bonds, or Substructures
General Description of the Expression Dialogs

Selected Displays the number of objects that are selected in the

currently active molecule area. Invisible hydrogens,
which are selected implicitly with the atoms they are
connected to, are not included in the count of selected
objects.
Pick by In addition to selecting items in the hierarchy, the fol-
lowing options allow you to define selections based on
different categories of items (e.g., a particular residue
type, a predefined set, anything within a radius of an
atom, etc). Boolean operations are available for com-
bining the selections with any hierarchical selections.
• Atoms—Available only in the Bond Expression
dialog. Displays the Atom Expression dialog for
selecting bonds based on an atom expression.
• Substructures—Available in the Atom Expression
and Bond Expression dialogs when a protein or a
structure extracted from a protein is displayed.
Displays the Substructure Expression dialog for
selecting atoms based on residue, water, or other
defined substructure.
• Sets—Displays the Sets Selection dialog for basing
selection on defined sets, a radius, chirality, and/or
conformation. The options available depend on the
Expression dialog from which the Sets Selection
dialog is launched.
• Types—Displays the Types dialog for basing
selection on particular types of atoms, bonds, or
residues (depending on the Expression dialog from
which the Sets Selection dialog is launched).
Show Expres- Activate to expand the dialog to display a field contain-
sion ing the selection expression. Deactivate to collapse the
dialog by hiding the expression field.
You type a new or modify the existing expression in
this field. If you do, press Apply. See SYBYL Objects
and Their Expressions (in the SPL Manual).
Create Set Defines a new set containing the selected items. Spec-
ify a name for the set. This new set is added to the list
of predefined sets in the Sets dialog. (Note: The new set
is temporary unless you save the molecule. Otherwise,
it is lost once the molecule is deleted from the display.)

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 6. Select Atoms, Bonds, or Substructures
General Description of the Expression Dialogs

Boolean Action The Boolean operators can be used to combine two

Buttons groups of selected items. These buttons appear only
when the Atom Expression or Substructure Expression
dialogs are accessed by clicking Pick by Atoms or
Substructures in another Expression dialog where
selections have been made.
• Intersect—Find the common items between the
selection identified in this dialog and the previous
selection. The remaining highlighted items are those
found in both groups of selected items.
• Remove—Subtract the items selected in this dialog
from the previous selection. The remaining
highlighted items are those found in the first group
of selected items, but not the second.
• Add—Add to the previous selection. The remaining
highlighted items are in either of the two groups of
selected items.

Usage Note: Atoms that are invisible cannot be selected and, therefore, cannot
be acted upon unless the operation affects the entire molecule area. For
example, if only the protein and water atoms within a 5 Å radius of a ligand are
currently visible, the Selection > Water operation will select only the visible
waters, not all of them. A subsequent deletion of the selected atoms will delete
only those few visible waters, leaving all others invisible, but still present.

Additional Information in the SPL Manual:

• Formats for Specifying Objects
• How to Specify an Atom Expression
• How to Specify a Bond Expression
• Monomer Sequence Specification
• Create Complex Expressions

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6. Select Atoms, Bonds, or Substructures
General Description of the Expression Dialogs

6.3.2 Atom, Bond, Residue Types

The contents of the Types dialog depends on the Expression dialog from which
it was launched.

In an Expression dialog, press Types.

Atom Types Residue Types

Type List Lists available types for the atoms, bonds, or residues.
• The Atom Types dialog displays a hierarchy of atom
names and types. It functions the same way as the
Expression dialog hierarchy in terms of making
selections and expanding/collapsing lists.
• When bonds are being selected based on atom
types, all bonds connected to specified atoms are
highlighted.
• Bond types include: 1 (single), 2 (double), 3
(triple), am (amide), ar (aromatic), du (dummy),
un (unknown, cannot determine from the parameter
tables), nc (non-chemical).
• The Bond Types and Residue Types dialogs are
simple lists of types. Click multiple items to select
them. Click again to remove from the selection.
Sort Alphabeti- Sorts the list of residues alphabetically when turned
cally activated. Available only in the Residue Types dialog.

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 6. Select Atoms, Bonds, or Substructures
General Description of the Expression Dialogs

Boolean Action The Boolean operators can be used to combine two

Buttons groups of selected items.
• Intersect—Find the common items between the
selection identified in this dialog and the previous
selection. The remaining highlighted items are those
found in both groups of selected items. Available
only when a selection has been made in the
Expression dialog from which this dialog was
launched.
• Remove—Subtract the items selected in this dialog
from the previous selection. The remaining
highlighted items are those found in the first group
of selected items, but not the second. Available only
when a selection has been made in the Expression
dialog from which this dialog was launched.
• Add—Add to the previous selection. The
highlighted items are in either of the two groups of
selected items.

Additional Information:
General Description of the Expression Dialogs

6.3.3 Sets for Atom, Bond, and Substructure Selection

The contents of the Sets Selection dialog depends on the Expression dialog from
which it was launched. Although the various Sets Selection dialogs are very
similar to each other in layout, there are differences. In the dialog description
below, these differences are noted.

In an Expression dialog, press Sets.

Atom Sets Substructure Sets

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General Description of the Expression Dialogs

Chirality Selects a set of atoms that have a particular chirality.

Available only in the Sets for Atom Selection dialog.
Sphere Selects a set of atoms that fall within the specified
radius of currently selected atoms. Available in the Sets
for Atom Selection and Sets for Substructure Selection
dialogs.
Built-In Sets Selects atoms that belong to a particular built-in set.
(Note that the Rings option will identify internal and
external ring systems.) See Built-in Sets on page 215
for definitions of these sets. Available in the Sets for
Atom Selection and Sets for Bond Selection dialogs.
Sets Selects atoms that are part of a global or local set. Use
the Ctrl key (Command on the Mac) to select multiple
items in the list. See Local Sets on page 212 and Global
Sets on page 209 for more information.
Conformations Selects substructures that form a particular conforma-
tional state in a protein. This list contains residue con-
formational states as defined in the macromol
dictionary. See the Dictionary Files description in the
Biopolymer Manual. Available only in the Sets for Sub-
structure Selection dialog.
Boolean Action The Boolean operators can be used to combine two
Buttons groups of selected items.
• Add—Add to the previous selection. The remaining
highlighted items are in either of the two groups of
selected items.
• Intersect—Find the common items between the
selection identified in this dialog and the previous
selection. The remaining highlighted items are those
found in both groups of selected items. Available
only when a selection has been made in the
Expression dialog from which this dialog was
launched.
• Remove—Subtract the items selected in this dialog
from the previous selection. The remaining
highlighted items are those found in the first group
of selected items, but not the second. Available only
when a selection has been made in the Expression
dialog from which this dialog was launched.

Additional Information:
General Description of the Expression Dialogs

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 6. Select Atoms, Bonds, or Substructures
General Description of the Expression Dialogs

6.3.4 Molecule Expression

The Molecule Expression dialog is used when the context calls for identifying a
molecule(s) on which to operate.

Molecule List List of currently displayed molecules.

Buttons to assist in selecting items in the list: select all,
invert selection, clear selection.

Additional Information:
General Description of the Expression Dialogs on page 64

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6. Select Atoms, Bonds, or Substructures
How to Use the Atom Expression Dialog

6.4 How to Use the Atom Expression Dialog

The purpose of this tutorial is to explore the functionality offered by the Atom
Expression dialog.

The topics specifically covered include:

• General Tools for Atom Selection on page 72
• Simple Atom Selection on page 73
• The Atom Expression on page 74
• Select Atoms by Type on page 75
• Select Atoms via Defined Sets on page 76
• Atom Selection Tools for Proteins on page 77

A Matter of Time: This tutorial requires 5 minutes of personal time.

Additional Information:
• General Description of the Expression Dialogs on page 64
• SYBYL Objects and Their Expressions (in the SPL Manual)
• The Selection Menu and Icons on page 59

6.4.1 General Tools for Atom Selection

Setup

1. It is always a good idea to clear the screen and reset the display before starting.

! > Delete Everything

! Click to reset all rotations and translations.

2. Load dicloxacillin.

! Click on the SYBYL toolbar.

! In the Open File dialog set the Files of Type to SYBYL Mol2.

! In the list of Bookmarks select [$TA_DEMO].

! In the Directory Navigation list select example.mdb.

! In the Selection list double-click dicloxacillin.mol2.

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 6. Select Atoms, Bonds, or Substructures
How to Use the Atom Expression Dialog

Simple Atom Selection

3. Invoke the Atom Expression dialog.

! Selection > Select Atoms or press .

! Ctrl+click (Command+click on the Mac) a few atoms in the molecule.

The selected atoms are highlighted on the screen. In the dialog the check boxes
for the selected atom are flagged, and a line below the list reports the number of
currently selected atoms.

! In the Atom Expression dialog, press (Select All).

All 49 atoms are selected in the dialog and highlighted on the screen.

! Press (Clear Selection).

0 atoms are selected.

! Select any three atoms in the dialog or Ctrl+click (Command+click on

the Mac) to select them in the molecule.
! Ctrl+click (Command+click on the Mac) one of the three atoms a
second time.

That atom is no longer selected or highlighted.

! Press the icon to invert the selection.

47 atoms are selected.

! Press to clear the selection.

Usage Notes:
• If multiple molecule areas are occupied, picking from the screen is
enabled only in the molecule area designated at the top of the dialog.
• When the dialog is invoked via the icon (Selection > Select
Atoms), the molecule area is set automatically to that of a pre-selected
atom or, if nothing had been selected, to the current default molecule
area as reported at the bottom of the SYBYL window (set via Options >
Set > Default Molecule Area).

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6. Select Atoms, Bonds, or Substructures
How to Use the Atom Expression Dialog

The Atom Expression

4. Selected atoms are stored in an atom expression. This information is accessible

at the bottom of the dialog.
! At the bottom of the Atom Expression dialog activate the Show Atom
Expression check box.
! Click one atom in the molecule to select it.

The Atom Expression field echoes the atom’s ID number.

! Ctrl+click (Command+click on the Mac) to select a few more atoms.

Each atom’s corresponding ID number is echoed within the parentheses in the

expression.

! Press to clear the selection.

The expression acknowledges that nothing is selected: M1(empty).

! Press to select all atoms.

An asterisk (*) appears between the parentheses. This represents all atoms in
the molecule.

74 SYBYL Basics SYBYL-X 2.1

 6. Select Atoms, Bonds, or Substructures
How to Use the Atom Expression Dialog

5. You can also type atom ID numbers directly into the field.

! In the expression field delete * then type 4,5,6,7 within the paren-
theses.
! Press Apply.

Nothing happens to the molecule until you press Apply. Four atoms are
highlighted.

! Press the icon.

! Deactivate the Show Atom Expression check box.

Refer to SYBYL Objects and Their Expressions (in the SPL Manual) for a
complete description.

6. Select Atoms by Type

! At the bottom of the Atom Expression dialog, click Types to display a

list of atom types.
! Activate the O check box.

! Click the + to expand the O category.

All oxygen atom types defined within SYBYL are selected in the list.

! Press Add to return to the Atom Expression dialog.

The five oxygens are highlighted in the molecule and in the dialog.

7. So far, you have added atoms to your selection. Now try subtracting the
carbonyl oxygens to keep only the other two.
! Press Types.

! In the Atom Types dialog, click the + to expand the O category again.

! Activate the check box for O.2 in the list.

! Press Remove.

Only two oxygens remain selected.

! Press to clear the selection.

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6. Select Atoms, Bonds, or Substructures
How to Use the Atom Expression Dialog

Select Atoms via Defined Sets

SYBYL includes a wide variety of rule-based sets that can be applied to select
atoms. Examples of these are Aromatic, H-bonds, Backbone, Sidechain, Rings,
etc. See Built-in Sets on page 215.

8. Select all atoms that are aromatic.

! In the Atom Expression dialog, click Sets to open the Sets for Atom
Selection dialog.
! Activate the Aromatic check box and press Add.

All carbons in the phenyl ring are selected.

! Activate the Show Atom Expression check box.

The field below the list shows the expression that is used to locate all (*)
aromatic atoms: {AROMATIC(*)}. Set names must always be surrounded by
braces.

! Press to clear the selection.

9. Locate all rings within this molecule.

! Press Sets.

! In the Sets for Atom Selection dialog, activate the Rings check box and
press Add.

Four rings are identified and the Atom Expression field has a defined
argument to locate all atoms within a ring.

10. Find all nitrogen atoms in rings.

You have already selected Rings in the Atom Types dialog, now select another
criteria.

! Press Types.

! In the Atom Types dialog, activate the N check box.

! Press Intersect.

The Intersect operator can be thought of as a true “AND” filter in that both
conditions must be met.

Two nitrogen atoms are now selected. This is because only two of the three
nitrogens are also part of a ring.

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 6. Select Atoms, Bonds, or Substructures
How to Use the Atom Expression Dialog

! In the Atom Expression dialog, deactivate the Show Atom Expression

check box.

11. This concludes the exercise.

! Press to clear the selection.

! Press Cancel to close the Atom Expression dialog.

6.4.2 Atom Selection Tools for Proteins

Most of the time selections in protein involve residues. See the How to Use the
Substructure Expression Dialog on page 82 for examples.

There are times, however, when the selection must consist of atoms, not full
residues. The following exercise is one such example.

1. Clear the screen.

! > Delete Everything

2. Load crambin from a file in SYBYL’s demo directory.

! Click on the SYBYL toolbar.

! In the Open File dialog set the Files of Type to PDB.

! In the list of Bookmarks select [$TA_DEMO].

! In the Selection list double-click 1crn.pdb.

Select Atoms via Defined Sets

3. Invoke the Atom Expression dialog.

! Selection > Select Atoms or press .

4. Invoke an operation that requires an atom selection.

! In the Atom Expression dialog click on the PHE13 check box.

The 11 atoms in PHE13 are highlighted.

5. Find all atoms that are within a 4 Å sphere of any PHE13 atom.

! Press Sets.

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6. Select Atoms, Bonds, or Substructures
How to Use the Atom Expression Dialog

! In the Sets for Atom Selection dialog activate Sphere and type 4 in the
field.
! Press Add.

All atoms within the specified radius are highlighted in the molecule. Notice
that the selection does not include complete residues.

6. In the dialog notice that some of the check boxes are colored to indicate partial
selection within the corresponding residues.

! In the dialog expand the hierarchy for any of the partially selected
residues to see the atom(s) selected within.

7. Reduce the current atom selection to sidechain atoms only. You will use a built-
in set defined for that purpose.
! Press Sets.

! In the Sets for Atom Selection dialog activate the Sidechain built-in set.

! Press Intersect.

19 atoms are selected: all sidechain atoms within a 4 Å sphere around any
PHE13 atom.

! If you are curious about the expression used to identify these atoms,
activate the Show Atom Expression check box.
! Press OK to exit the Atom Expression dialog with the current selection.

8. Color the selected atoms.

! Use the icon’s arrow to select and apply your favorite

contrasting color.

Notice that the color icon’s image has changed to match the color you selected.
This is now the default color until you select another one.

This concludes the exercise.

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 6. Select Atoms, Bonds, or Substructures
How to Use the Bond Expression dialog

6.5 How to Use the Bond Expression dialog

A Matter of Time: This tutorial requires a couple of minutes of personal time.

Additional Information:
• General Description of the Expression Dialogs on page 64
• SYBYL Objects and Their Expressions (in the SPL Manual)

6.5.1 Setup
1. Load dicloxacillin from a file in SYBYL’s demo directory.

! Click on the SYBYL toolbar.

! In the Open File dialog set the Files of Type to SYBYL Mol2.

! In the list of Bookmarks select [$TA_DEMO].

! In the list of Directory Navigation select example.mdb.

! In the Selection list double-click dicloxacillin.mol2.

2. Invoke a SYBYL feature that affects bonds.

! Edit > Bond > Modify Type

! Select TYPE and press OK.

SYBYL opens the Bond Expression dialog.

! If multiple molecules are currently on the screen, you must designate

the molecule area of interest at the top of the dialog.

6.5.2 Select a Bond on the Screen

! Hold the Ctrl key (Command on the Mac) and click two atoms that
are bonded to each other.

The corresponding bond is highlighted in the dialog. An information line below

the hierarchy reports that 1 bond is currently selected.

! To clear the selection click anywhere on the SYBYL backdrop or

press the icon in the dialog.

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6. Select Atoms, Bonds, or Substructures
How to Use the Bond Expression dialog

6.5.3 Select all Bonds Connected to an Atom

! In the Bond Expression dialog, press Atoms.

The Atom Expression dialog is posted and automatically set to the same
molecule area.

! Click on the nitrogen in the fused (β-lactam) ring system then press
Add.

The three bonds between the nitrogen and its highlighted neighbors are selected
in the dialog.

! Press the icon to clear the selection.

6.5.4 Select Bonds by Type

! In the Bond Expression dialog, press Types.

All bond types are presented in the Bond Types dialog.

! Press ar then Add.

All aromatic carbons are highlighted, and the dialog reports that 6 bonds are
currently selected.

! Press the icon to clear the selection.

6.5.5 Select Bonds via Defined Sets

! In the Bond Expression dialog, press Sets.

The Sets for Bond Selection dialog presents named definitions that can be used
to identify bonds.
• A few built in sets can be applied to bonds. See Built-in Sets on page
215.
• Special purpose sets are defined in the macromol dictionary. See Global
Sets in the Biopolymer Dictionary on page 210.

Most defined sets pertain to biopolymers. However, one of them can be used as
an example for this tutorial: Rings.

! In the Built-in Sets section, activate Rings then press Add.

On the screen all ring atoms are highlighted. In the dialog the 19 bonds between
these atoms are selected.

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 6. Select Atoms, Bonds, or Substructures
How to Use the Bond Expression dialog

! Press the icon.

This concludes the exercise about the Bond Expression dialog.

! Press Cancel to close the dialog.

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6. Select Atoms, Bonds, or Substructures
How to Use the Substructure Expression Dialog

6.6 How to Use the Substructure Expression Dialog

Selecting a substructure can be done easily by double-clicking any of its atoms.
The purpose of this tutorial is to explore the functionality offered by the dialog.

A Matter of Time: This tutorial requires a couple of minutes of personal time.

Additional Information:
• General Description of the Expression Dialogs on page 64
• SYBYL Objects and Their Expressions (in the SPL Manual)

6.6.1 Setup
1. Load crambin from a file in SYBYL’s demo directory.

! Click on the SYBYL toolbar.

! In the Open File dialog set the Files of Type to PDB.

! In the list of Bookmarks select [$TA_DEMO].

! In the Selection list double-click 1crn.pdb.

2. Label the residues.

! Use to label the substructures (Molecules > Substructure).

3. Invoke a SYBYL feature that affects substructures.

! Biopolymer > Composition > Mutate Monomers

SYBYL opens the Sequence Expression dialog.

! If multiple molecules are currently on the screen, you must designate
the molecule area of interest at the top of the dialog.

6.6.2 Select Residues on the Screen

! Click on any atom of a single residue. The most reliable way to select
a particular residue is to select its alpha carbon, the atom bearing the
residue’s substructure label.
! To add to the selection, hold the Ctrl key (Command on the Mac)
while you click on another residue.

Below the hierarchy in the dialog a line reports the number of substructures
currently selected.

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 6. Select Atoms, Bonds, or Substructures
How to Use the Substructure Expression Dialog

! To clear the selection click anywhere on the SYBYL backdrop or

press the icon in the dialog.

6.6.3 Select Residues by Name

! In the Sequence Expression dialog, click and drag to select VAL8
through ASN12.

All atoms in the selected residues are highlighted in the display area. Below the
hierarchy in the dialog a line reports that 5 substructures are currently selected.

! Press the icon (Clear Selection).

6.6.4 Select Residues by Type

! In the Sequence Expression dialog, click Types to open the Residue
Types dialog.

The Residue Types dialog lists all possible monomer types available in the
dictionary. The standard amino acids are in the leftmost column. You can also
Sort Alphabetically to facilitate selection.

! In the Residue Types dialog, select CYS in the list and press Add.
The six CYS residues are highlighted with the green selection markers.

! Press the icon (Clear Selection).

6.6.5 Select Residues via Defined Sets

! In the Sequence Expression dialog, press Sets to open the Sets for
Substructure Selection dialog.

All sets in this dialog are substructure sets, which means that they apply to
entire residues. The list of sets is compiled from two sources:
• Special purpose sets whose definitions are stored in the macromol
dictionary. See Global Sets in the Biopolymer Dictionary on page 210.
• Sets that were created automatically by SYBYL upon reading the PDB
file. See sets created upon reading a PDB file (in the Biopolymer
Manual).

Selection based on conformational states, as defined in the dictionary, can also

be made in this dialog.
! Select HELIX_H1_PDB from the Sets list and press Add.

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6. Select Atoms, Bonds, or Substructures
How to Use the Substructure Expression Dialog

All atoms in residues in one of the two helices are highlighted with the green
selection markers.

This concludes the exercise about the Substructure Expression dialog.

! Press Cancel to close the dialog.

84 SYBYL Basics SYBYL-X 2.1

 7. Clear and Reset the SYBYL Display
• Clear the SYBYL Screen and Delete Objects on page 86
• Clear the SYBYL Screen on page 86
• Delete Selected Molecules, Atoms and Backgrounds on page 86
• Delete Molecules on page 86
• Delete Atoms on page 87
• Delete Backgrounds on page 88
• Delete Whatever is Selected on page 89
• Reset Scaling, Translation, and Rotation on page 90

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7. Clear and Reset the SYBYL Display
Clear the SYBYL Screen and Delete Objects

7.1 Clear the SYBYL Screen and Delete Objects

The icon consists of two buttons:
• Click the X to delete whatever is currently selected.
• Use the pull-down arrow to specify what will be deleted.

7.1.1 Clear the SYBYL Screen

Delete absolutely everything in the SYBYL graphics window. This operation
does not affect molecules displayed in a molecular data explorer’s 3D Viewer.

Menubar: Edit > Delete Everything

Toolbar Icon: Click the icon’s arrow and select Delete Every-
thing.
Command: ZAP * to remove all molecules and associated back-
ground images followed by BACKGROUND DELETE * to
remove all remaining independent background images.

All molecules and all graphics images, known as backgrounds, are removed
from the SYBYL graphics window.

7.1.2 Delete Selected Molecules, Atoms and Backgrounds

For information on how to select objects refer to:
• The Selection Menu and Icons on page 59
• Select Atoms, Bonds, or Substructures on page 57

Delete Molecules

Delete the specified molecule(s) in the SYBYL graphics window. This

operation does not affect molecules displayed in a molecular data explorer’s 3D
Viewer.

Menubar: Edit > Delete > Molecules

then specify the molecule(s) to delete.
Or select atom(s) in one or more molecules then
Edit > Delete > Selected Molecules

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 7. Clear and Reset the SYBYL Display
Clear the SYBYL Screen and Delete Objects

Toolbar Icon: Click the icon’s arrow and select Molecules

then select in the list of molecule(s).
Or select atom(s) in one or more molecules then click
the icon’s arrow > Selected Molecules.
Command: ZAP mol_expr

Background images, such as MOLCAD surfaces, associated with the deleted

molecules are removed from the screen as well.

How to delete a UNITY query that does not contain any atoms?

Menubar: Edit > Delete > Molecules then select the query in
the list of molecule(s).
Toolbar icon: Click the icon’s arrow and select Molecules
then select the query in the list of molecule(s).
Command: ZAP mol_area

Delete Atoms

Delete the specified atoms. Menubar and toolbar require pre-selection of atoms.

When using the graphical interface, invisible hydrogens connected to the

deleted atoms are also deleted.

Menubar: Select atom(s) in one or more molecules then

Edit > Delete > Selected Atoms.
The selected atoms and any invisible hydrogens con-
nected to them are deleted.
Toolbar Icon: Select atom(s) in one or more molecules then click the
icon’s arrow and select Selected Atoms.
The selected atoms and any invisible hydrogens con-
nected to them are deleted.
Atom Right-Click: • > Delete Atom—If the clicked-on atom is not
selected, only that atom is deleted along with any
invisible hydrogens connected to it.
• > Delete Selected Atoms—If the clicked-on
atom is selected, all selected atoms, regardless of
molecule area, are deleted along with any invisible
hydrogens connected to them.

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7. Clear and Reset the SYBYL Display
Clear the SYBYL Screen and Delete Objects

Command: REMOVE ATOM atom_expr

Issue this command for each molecule in which atoms
must be deleted, making sure to include the appropriate
molecule area within the atom expression.
See How to Specify an Atom Expression (in the SPL
Manual).

Deleting atoms also removes all bonds involving the deleted atom(s) and any
features (normal, plane, constraint) attached to them. SYBYL renumbers atoms
and bonds to reflect the removal of objects from the molecular description. If a
deleted atom was a member of a static set, the set membership is updated.
Deleting all atoms is equivalent to deleting the molecule.

Unless an entire molecule is deleted, its associated background images, such as

MOLCAD surfaces, remain on the screen.

See also Delete Atoms or Atom Attributes on page 139.

Delete Backgrounds

Delete one or more background object. This functionality is enabled on the

menubar and icon only if at least one background is present.

A background is any graphics object that is not a molecule. Examples are

CoMFA contours, and MOLCAD surfaces and ribbons.

Menubar: Edit > Delete > Backgrounds (Surface, Ribbon,

etc.)
Select the background(s) to be deleted or ALL.
Toolbar Icon: Click the icon’s arrow and select Backgrounds.
Select the background(s) to be deleted or ALL.
Surface or Ribbon This option is available for MOLCAD-generated sur-
right-click: faces, ribbons, cones, and field lines.
• > Delete Surface—If the clicked-on MOLCAD
object is not selected, only that object is deleted.
• > Delete Selected Surfaces—If the clicked-on
MOLCAD object is selected, all selected MOLCAD
objects are deleted.
Command: BACKGROUND DELETE background_id
Specify the ID number of the background to be deleted
or * to delete all backgrounds at once. To find the ID
numbers of individual background images type LIST
BACKGROUND.

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 7. Clear and Reset the SYBYL Display
Clear the SYBYL Screen and Delete Objects

Background deletion cannot be undone.

Delete Whatever is Selected

Delete whatever is selected, atoms, surfaces or both. This functionality is

enabled on the menubar and icon only if at least one atom or surface has been
selected.

Menubar: Select atom(s) in one or more molecules and/or select

surface(s) then
Edit > Delete > Selected
Toolbar Icon: Select atom(s) in one or more molecules and/or select
surface(s) then
Click to delete all selected objects.
If nothing had been selected before clicking the X,
nothing will be deleted.

Only atoms, MOLCAD surfaces and ribbons as well as potential surfaces can be
selected and deleted in this manner.

Read about The Selection Menu and Icons on page 59.

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7. Clear and Reset the SYBYL Display
Reset Scaling, Translation, and Rotation

7.2 Reset Scaling, Translation, and Rotation

7.2.1 Reset All
Reset SYBYL’s graphics window to the original scale, rotation, and translation
settings.

Menubar: View > Transformations > Reset All

Toolbar Icon:

7.2.2 Reset Selectively

Reset all or selective scale, rotation, and translation settings.

Toolbar Icon:

Command: STATIC RESET

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 7. Clear and Reset the SYBYL Display
Undo the Last Operation

7.3 Undo the Last Operation

Each molecule area has a single level stack associated with it. Prior to an
operation that affects a molecule’s coordinates, or atom and bond definitions,
the current state is saved on this stack. If you choose to reverse the action of a
command, this data is available to return to the previous state.

Menubar: Not accessible from the menubar.

Command: RECOVER mol_area
UNDO (identical to RECOVER M*)

Notes:
1. The state saved to the stack includes coordinates, atom and bond definitions.
2. UNDO and RECOVER do not reverse the effect of labels or colors.
• If you want to reverse the effect of a labeling operation, use View >
Unlabel.
• You can not reverse the effect of coloring operations. If you have a color
scheme you wish to save, you need to save the molecule with that color
scheme.
3. The automatic saving to the stack is controlled by the SET AUTOSAVE
command (described in the Graphics Manual).

SYBYL-X 2.1 SYBYL Basics 91

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 8. The SYBYL Sketcher

Use the SYBYL Sketcher to draw a new molecule or modify an existing

structure.
• Sketch a Small Molecule Tutorial on page 94
• Access the Sketcher on page 101
• Sketching Techniques on page 101
• Sketcher Toolbars on page 105

Additional Information:
Options of the Edit menu allow you to add, define, modify, copy, and delete
various molecular components.
• Molecules: Build, Delete, Modify on page 109
• Substructures: Delete, Modify on page 131
• Atoms: Add, Delete, Modify on page 135
• Bonds: Add, Delete, Modify on page 147
• Geometry: Measure, Modify, Define Features on page 153

SYBYL-X 2.1 SYBYL Basics 93

8. The SYBYL Sketcher
Sketch a Small Molecule Tutorial

8.1 Sketch a Small Molecule Tutorial

This tutorial introduces the most common features of SYBYL’s sketcher. See
Sketcher Toolbars on page 105 for a full description.

8.1.1 Preface
In this tutorial, you will build and minimize Atropine by building the most
complex ring system first and then adding the substituents. Typically, molecular
fragments from the Standard Fragment Library are used to quickly construct
ring systems with good geometry. However, in order to better demonstrate
SYBYL’s sketching capabilities, you will use the Sketch Molecule menu
items to construct and optimize the most complex ring system.

After completing this tutorial, you will be able to:

• Draw a ring
• Draw a chain
• Add substituent groups
• Check and assign chirality

Before performing the following tutorial you should be familiar with the
graphics functions of SYBYL. If necessary, refer to the Quick Reference
section in the Graphics Manual for a summary.

A Matter of Time: This tutorial requires about 10 minutes of personal time.

8.1.2 Set Up
1. It is always a good idea to clear the screen and reset the display before starting.

! > Delete Everything

! Click to reset all rotations and translations.

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 8. The SYBYL Sketcher
Sketch a Small Molecule Tutorial

! Use to set the screen mode to Full.

8.1.3 Enter the Sketching Mode

2. Display the sketch menus and select M1 as the work area in which to build the
molecule.

! File > New > Small Molecule or click .

A series of toolbars are added to the SYBYL window. You may reposition them
along any edge of the SYBYL window. See Sketcher Toolbars on page 105 for
a full description.

You are automatically placed in Draw mode, as indicated by , so you can

begin sketching immediately.

3. Display a grid to aid in building the molecule to scale. The spacing between
grid points is 1.54 Å, the sp3 carbon to sp3 carbon bond length. The grid scales
with the molecule in order to show the correct bond length.

! Click to display the grid.

Note: If the grid gets in your way, toggle it off by pressing again.

8.1.4 Sketch the Ring System

4. Build the piperidine ring as follows:

! Click in the middle of the screen.

SYBYL displays a “+” representing an unconnected atom. The small box

around it indicates that this atom is the current attachment point to which the
next sketched atom will be attached.
! Click a point above the first atom and approximately one grid spacing
to the right (see atom 2 in the figure below).

SYBYL draws a bond to the newly created second atom.

! Continue sketching the 6-membered ring by clicking appropriate

points on the screen.
! Close the ring by selecting atom 1 again.

When you close the ring by picking atom 1, no atom is highlighted, indicating
that continuous Draw mode is temporarily deactivated. Continuous mode is
always suspended when an existing atom is chosen, whether it is the current

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8. The SYBYL Sketcher
Sketch a Small Molecule Tutorial

atom of attachment or another atom. In the former case, no bond is drawn; while
in the latter case, a bond is drawn and then continuous draw mode is deacti-
vated.

5. Change the type of atom 1 to a nitrogen.

! On the second toolbar (showing various atomic symbols), click N.

! On the first toolbar, click .

! Click atom 1 on the sketched molecule.

SYBYL displays a label indicating that the type has been successfully changed
and the atom is colored blue.

6. Introduce a third dimension to the molecule.

! Click and hold down the Left mouse button and drag the cursor up to
rotate the molecule about the X axis until it has an orientation similar
to that shown in the figure below.

7. Add the bridge across the ring.

! On the second toolbar, click C then click to go back to draw

mode.
! Click atom 2 to make it the current attachment atom.

! Click a point below atom 2 and then another point diagonal to the
new atom.
! Click atom 6 to close the ring.

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 8. The SYBYL Sketcher
Sketch a Small Molecule Tutorial

8. Move carbon 4 down to give the ring a chair conformation.

! Click , then on atom 4 then on a point below it and below the

plane of the ring.

9. Clean up the ring system.

! On the first toolbar, click .

The molecule’s geometry is optimized using the Tripos force field.

8.1.5 Add a Chain

10. Center the molecule on the screen.

! Click to center the molecule.

! Rotate the molecule until its orientation is similar to that shown in the
figure below.

11. Add a carbon chain to the ring.

! Click atom 4 as the new attachment atom.

! Sketch the chain by clicking successive points at approximate

locations on the screen for atoms 9 through 13.
! Click atom 13 again to deactivate continuous Draw mode and end the
chain.

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8. The SYBYL Sketcher
Sketch a Small Molecule Tutorial

12. Draw a double bond for the carbonyl group.

! Click atom 10 as the new point of attachment and then click a point
above the atom.
! Click atom 10 again.

The double bond appears and continuous Draw mode is deactivated, since an
existing atom was chosen.

13. Add a carbon to the nitrogen.

! Click atom 1 (N), then a point to its left.

! Click that new atom again to deactivate continuous Draw mode.

14. Sketch the ester and hydroxyl groups.

! On the second toolbar, click O then click .

! Click each of the three atoms: 9, 13, and the end of the double-bond.

The atoms are labeled with an O and colored red to reflect the change.

8.1.6 Add a Phenyl Group

15. Add a phenyl ring to the molecule.

! On the sketcher’s third toolbar (showing various groups), click

PHENYL.
! In the structure, click atom 11.

16. Center the molecule.

! Click .

! Compare your sketch with atropine. (Hydrogens will be added later.)

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 8. The SYBYL Sketcher
Sketch a Small Molecule Tutorial

8.1.7 Check the Chirality

17. Make sure that atom 11 has a chirality of S.

! Click and click atom 11.

! Select S and press OK.

If atom 11 was already an S chiral center nothing happens. If the R chiral center
has been sketched, the carbon is inverted to assume the proper stereochemistry.

8.1.8 Clean Up the Model

18. Clean up the model.

! Click .

19. Add the necessary hydrogens to all unfilled valences.

! Click to fill all open valences with hydrogens.

All atom and bond types are automatically converted to SYBYL types, based on
the connectivity prior to adding hydrogens.

20. Exit the sketching mode.

! On the first toolbar click .

A final clean up is done automatically when you exit the sketcher.

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8. The SYBYL Sketcher
Sketch a Small Molecule Tutorial

8.1.9 Save the Sketched Molecule

21. Name the molecule.

! Right-click on any atom and select Rename Molecule.

! Type atropine and press OK.

22. Save the full description of the molecule in a text file.

! File > Export File ( )

! In the Save Molecule dialog, by default, atropine appears in the File

field.
! By default, the Format is set to MOL2.

! Press Save.

A file named atropine.mol2 is created in the current directory.

23. This concludes the small molecule sketching tutorial.

In this tutorial, you built and minimized atropine by building the most complex
ring system first and then adding the substituents.

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 8. The SYBYL Sketcher
Access the Sketcher

8.2 Access the Sketcher

Menubar: File > New > Small Molecule
or Edit > Molecule > Sketch
See Sketcher Toolbars on page 105.
Toolbar Icon:

Command: SKETCH mol_area

File > New > Small Molecule always uses the first empty molecule area.

Edit > Molecule > Sketch and determine the molecule area to use as
follows:
• If nothing is selected, the Sketcher uses the first empty molecule area.
• If one or more atoms are selected in the same molecule area, the
Sketcher is launched for that molecule area. This is how to use the
Sketcher to modify an existing molecule.
• If atoms were selected in multiple molecule areas you will be prompted
to specify which molecule area the Sketcher will operate on.
• All hidden atoms in the selected molecule are made visible upon
invoking the Sketcher.

Additional Information:
• Sketching Techniques on page 101
• Sketcher Toolbars on page 105
• Edit > Clean-Up Molecule > 3D Geometry (Concord) for fast
conversion of 2D coordinates to 3D (in the Concord Manual)
• Tailor subject GRID to customize the displayed grid

8.2.1 Sketching Techniques

The following sections discuss some basic ideas and helpful techniques for
using the Sketcher.

You can start sketching with an atom or a fragment.

Important: You can not start sketching with a chemical group.

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8. The SYBYL Sketcher
Access the Sketcher

Always Review the Sketched Model

Although flexible enough to enable building any structure, the Sketcher does
have enough chemical sense to warn you when you have done something
unnatural. For example, SYBYL displays a message if the valence of an atom is
about to be exceeded. It is your decision to continue or not.

About Continuous Drawing Mode

You can stop the continuous drawing mode (also referred to as “pen up
movement”) by doing one of the following:
• To cancel the selection of a point of attachment, click the last atom
drawn.
You can then move the cursor to another part of the molecule without
drawing a bond. When you pick a new point of attachment, continuous
drawing mode is turned on again.
• Click an existing atom. A bond is drawn from the current atom to this
existing atom and then the pen up movement is initiated.

Atomic Symbols Only

SYBYL designates the atom types with only the atomic symbols, in order to
eliminate the burden of having to decide the proper SYBYL atom type.

Atom Types

You can change the atom types in two different ways:

Method One: Change the default atom type, before adding the new atom to the
model:
1. On the second toolbar, click the desired atomic symbol.
If the atom type is not listed, click More to display a periodic table and
select the desired atomic symbol. The table is color-coded using the SYBYL
atom type coloring scheme. Once a selection is made, click X in the upper
corner to close the table. (Note that the selected atomic symbol now appears
as a button below the More button on the toolbar.)
2. Click in the display area to add a new atom of that type.

Subsequent atoms have the new atom type until you select a different atomic
symbol. Use this technique if you want to draw a chain of atoms, other than
carbons.

Method Two: Modify the type of an existing atom:

1. On the second toolbar, click the desired atomic symbol.

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 8. The SYBYL Sketcher
Access the Sketcher

If the atom type is not listed, click More to display a periodic table and
select the desired atomic symbol. The table is color-coded using the SYBYL
atom type coloring scheme. Once a selection is made, click X in the upper
corner to close the table. (Note that the selected atomic symbol now appears
as a button below the More button on the toolbar.)
2. On the first toolbar, click .
3. Click the atom whose type you want to change.

SYBYL updates the atom type.

Branching

To draw an atom not connected to the last atom displayed, a pen up action must
be signified by choosing this last (highlighted) atom again. SYBYL removes the
highlighting and temporarily turns off the continuous draw mode. When you
choose a new point of attachment, SYBYL automatically turns the continuous
drawing mode on and you can add a new chain of atoms.

If you select a point of attachment in error, click that atom again to initiate the
pen up movement. You can now select a new point of attachment.

Edit Existing Molecules

Existing molecules or fragments can be brought into the sketcher in order to

make quick modifications. When the sketcher is exited or the clean-up option
selected, only the part of the molecule that changed is cleaned up. The rest of
the molecule maintains its current geometry. You can disable this option by
setting Tailor variable SKETCH AGGREGATES to OFF. With this option, the
whole molecule is considered in the clean up phase.

Label and Color

In order to make different atom types easily identified, heteroatom labeling and
molecule color, coded by atom type, are the sketcher defaults.

Multiple Bonds

Draw the single bond, then do one of the following:

• If the last atom drawn is one of the atoms involved in the double bond,
select the target atom and a second line appears between the two atoms
designating the double bond. Since the target atom is an existing atom,
continuous drawing mode is temporarily turned Off and a new point of
attachment must be chosen before drawing commences again.

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8. The SYBYL Sketcher
Access the Sketcher

• If neither atom defining the double bond is currently selected, turn Off
continuous drawing mode by picking the last atom drawn a second time.
Select one of the atoms of interest as the new point of attachment. Pick
the target atom for the double bond and a double line appears between
the two atoms. As mentioned above, since the target atom is an existing
atom, drawing mode is temporarily suspended.

The same strategy can be repeated for sketching triple bonds. Aromatic bonds
are designated by alternating single and double bonds within the ring.

Rings

Sketch the backbone on the ring by picking points at appropriate positions on

the screen. To close the ring select the first atom of the ring again, thereby
causing a bond to be drawn between this atom and the last atom drawn. Since
this ring closure atom is an existing atom, SYBYL temporarily stops the
continuous draw mode, so you can choose a new point of attachment. To add a
bond to the current atom, select that atom again.

Z Coordinate

Molecules are drawn flat until you rotate the structure. Any atom added subse-
quent to a rotation assumes the transformed Z-coordinate of the atom to which it
is bonded. Unconnected atoms are always two-dimensional since there is no
reference point.

To add a third dimension to the molecule, apply rotations to the model. Once an
atom has a Z-coordinate, any subsequent atoms attached to it are drawn in the
same Z-plane. For example, if a rotation precedes moving an atom ( ), the
atom being moved is drawn in a different plane from the rest of the molecule.
Many different conformations of a molecule can be achieved with this method,
such as chair or boat cyclohexane.

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 8. The SYBYL Sketcher
Sketcher Toolbars

8.3 Sketcher Toolbars

Access:
• File > New > Small Molecule
• Edit > Molecule > Sketch
•

Usage Notes:
• To modify an existing molecule select one of its atoms before invoking
Edit > Molecule > Sketch or the icon. Otherwise the Sketcher
will use the first empty molecule area to draw a new structure.
• To build upon a chemical fragment you must retrieve the fragment
before accessing the Sketcher. See Load Fragments from the Library on
page 224.
• The clean up method to be used when exiting the Sketcher must
specified before accessing the Sketcher. See Tailor variable SKETCH
CLEAN_UP in the Tailor Manual. The default method (6_MINIMIZE)
starts by fixing non-cyclic bond lengths and valences angles and rotating
non-cyclic bonds to escape atomic overlaps. It then optimizes the
geometry of the entire molecule by performing an energy minimization
using the Tripos force field.

The Sketcher has 3 toolbars of icons grouped as follows:

• Sketching Functions — Activities necessary to sketch a structure. See
Sketching Functions Toolbar below for descriptions.
• Atomic Symbols — Pick one of these atomic symbols to indicate the
atom type to draw. If the atom type is not listed, click More to display a
periodic table and select the desired atomic symbol. The table is color-
coded using the SYBYL atom type coloring scheme. Once a selection is
made, click X in the upper corner to close the table. (Note that the
selected atomic symbol now appears as a button below the More button
on the toolbar.)
• Groups — Substructures defined in the Group Library. Groups have
predefined attachment points. (Refer to Group Library on page 229 for
more information.)
Usage Note: you cannot start sketching with a chemical group. An atom
must exist as an attachment point before a functional group can be
added.

A toolbar can be moved to the top or the right side of the display area by
clicking on the dashed line and dragging it to the new location.

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8. The SYBYL Sketcher
Sketcher Toolbars

Toolbars can be reordered by dragging one at a time to the last position (closest
to the display area). You can also combine toolbars by dragging one over the
other. (This is what always occurs if you move more than one toolbar to the top
of the display area.)

8.3.1 Sketching Functions Toolbar

Activates the continuous drawing mode, the default action,

with the cursor defined as a carbon atom.
To draw a chain of carbons:
• Click a point on the screen where the first atom is to be
located; a cross appears.
• Click another point on the screen; that point appears
and SYBYL draws a line (bond) between the two
atoms.
• Continue clicking until you reach the desired chain.
Note that the current atom of attachment is always high-
lighted.
Places you in modify mode. Clicked atoms are replaced by
the atom selected in the second toolbar.
Prompts you for the atom to move and its new location.
The atom, and all bonds connected to it, are moved to the
new location. This mode remains active until you select
another option. This capability is useful when building a
particular conformer.
Deletes atoms, and bonds connected to them, from the
molecule being sketched. This mode remains active until
you select another option.
Removes a bond from the drawn structure. You must
select two bonded atoms. This mode remains active until
you select another option.
Undo: reverses the last operation, restoring the molecule
to its previous state.
Centers the molecule on the screen.

Adjusts molecule geometry according to the method speci-

fied via the Tailor variable SKETCH CLEAN_UP. Also
determines the proper atom hybridization, based upon
bond type and atom type of connected atoms. No matter
which option is chosen for clean-up, the atom and bond
type conversion is always done. By default,
Adds hydrogens to all unfilled valences.

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 8. The SYBYL Sketcher
Sketcher Toolbars

Removes all hydrogens in the sketched molecule.

Deletes the entire molecule being sketched.

Specifies whether a chiral center is R or S.

Modifies the torsion angle of four connected atoms.

Modifies the bond angle of three connected atoms.

Toggles the grid on and off. Use the grid to aid sketching.
Spacing between grid points is 1.54 Å, the approximate
length of a carbon-carbon single bond.
In the Command Console type a name for the molecule
being sketched. The Sketcher will then automatically
return to the drawing mode.
Performs clean up procedure and assigns SYBYL atom
types (see description for the clean up tool).

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 9. Molecules: Build, Delete, Modify

Use the options under the Edit menu to build, copy, and modify molecules.
• Copy or Move Atoms Between Molecule Areas on page 110
• Copy Atoms from one Molecule Area to Another on page 110
• Extract Atoms from one Molecule Area to Another on page 111
• Combine Two Molecules Into One on page 112
• Fuse Atom Pairs from Separate Molecules on page 116
• Ring Fusion Tutorial on page 117
• Join Two Atoms from Separate Molecules on page 116
• Merge Atoms from Separate Molecules on page 112
• Average Multiple Conformations on page 122
• Delete a Molecule on page 123
• Name or Rename a Molecule on page 124
• Chirality: Determine and Modify on page 125
• Determine Chirality on page 125
• Invert Chirality on page 126
• Reflect Atoms Through a Plane on page 126
• Modify Molecule Attributes on page 128
• Center of Rotation on page 128
• Molecule Name on page 128
• Molecule Type on page 128
• Molecule Root Atom on page 128
• Comment Associated with a Molecule on page 129

Additional Information:
• The SYBYL Sketcher on page 93
• The Edit menu (listed in the SYBYL Reference Guide)
• Substructures: Delete, Modify on page 131
• Atoms: Add, Delete, Modify on page 135
• Bonds: Add, Delete, Modify on page 147

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Copy or Move Atoms Between Molecule Areas

9.1 Copy or Move Atoms Between Molecule Areas

• A copy operation preserves the content of the source molecule area.
• An extract operation removes the specified atoms from the source
molecule area.

9.1.1 Copy Atoms from one Molecule Area to Another

Make an exact copy of all atoms selected in one molecule area and place the
copy in another area (by default the first empty area), replacing the content of
the target area. Associated data structures (properties, colors, sets) are also
copied.

When using the graphical interface, invisible hydrogens connected to the copied
atoms are also copied.

Menubar: Select atoms in a single molecule area then Edit >

Copy and specify the target molecule area.
The selected atoms and any invisible hydrogens con-
nected to them are copied.
Toolbar Icon: Select atoms in a single molecule area, click , then
specify the target molecule area.
The selected atoms and any invisible hydrogens con-
nected to them are copied.
Right-Click Any Right-click any atom > Copy Molecule
Atom The entire molecule, including hidden atoms, is copied.
Right-Click Select atoms in a single molecule area then right-click a
Selected Atoms selected atom > Copy Selected and specify the target
molecule area.
The selected atoms and any invisible hydrogens con-
nected to them are copied.
Command: COPY origin_atom_exp target_area
• origin_atom_exp—Molecule area to duplicate (e.g.,
M1) or atom expression (e.g., M1(1,2,3,5,10) speci-
fying the atoms to copy. All specified atoms,
whether visible or not, are copied.
• target_area—Molecule area to receive the copied
structure/atoms.

If atomic charges were present in the origin molecule, and not all atoms were
copied, the charges in the target area are marked invalid and will not be used by
subsequent SYBYL operations. You may validate these charges manually via
the command: CHARGE mol_area VALIDATE.

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9.1.2 Extract Atoms from one Molecule Area to Another

Cut the selected atoms from one molecule area and move them to another area
(by default the first empty area), replacing the content of the target area.

When using the graphical interface, invisible hydrogens connected to the

extracted atoms are also moved.

Menubar: Select atoms in a single molecule area then Edit >

Extract and specify the target molecule area.
The selected atoms and any invisible hydrogens con-
nected to them are moved.
Right-Click Any Right-click any atom > Move Molecule and specify
Atom the target molecule area.
The entire molecule, including hidden atoms, is moved.
Right-Click Select atoms in a single molecule area then right-click a
Selected Atoms selected atom > Extract Selected and specify the tar-
get molecule area.
The selected atoms and any invisible hydrogens con-
nected to them are moved.
Command: EXTRACT atom_expr target_mol_area
All specified atoms, whether visible or not, are moved.
If atom_expr does not specify a molecule area, the
default molecule area is used.

If atomic charges were present in the origin molecule, the atoms still bear the
same charges after the extraction. However, charges in both molecules are
marked invalid and will not be used by subsequent SYBYL operations. You
may validate these charges manually via the command: CHARGE mol_area
VALIDATE.

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9.2 Combine Two Molecules Into One

• Merge Atoms from Separate Molecules on page 112
• Join Two Atoms from Separate Molecules on page 116
• Fuse Atom Pairs from Separate Molecules on page 116
• Ring Fusion Tutorial on page 117
• Average Multiple Conformations on page 122

9.2.1 Merge Atoms from Separate Molecules

Merging combines a copy of selected atoms in the source molecule area with
the contents of the target area. Example of use: combining a docked ligand pose
and the protein active site into a single molecule area.

When using the graphical interface, invisible hydrogens connected to the

merged atoms are also merged.

Menubar: Select atoms in a single molecule area then Edit >

Merge and specify the target molecule area.
The selected atoms and any invisible hydrogens con-
nected to them are merged with the content of the target
area.
Command: MERGE atom_expr target_area
All specified atoms, whether visible or not, are moved.
If atom_expr does not specify a molecule area, the
default molecule area is used.

Check the output displayed in the console for messages about the merge.
Special conditions apply when merging non-unique atoms and features.
• Merged Atoms and Associated Data Structures
• Unique Versus Non-Unique Atoms
• Example of Merging Non-Unique Atoms

Tip: If either of the molecules had been rotated and/or translated, use View >
Transformations > Freeze to transform the coordinates before merging.

Additional Information:
• Combine Two Molecules Into One on page 112
• Copy or Move Atoms Between Molecule Areas on page 110

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Merged Atoms and Associated Data Structures

When you merge atoms most of the data structures associated with the
molecular description are maintained during the merge.
• Atoms
• Maintained: SYBYL atom type and atom name, alternate atom type
(AMBER/Kollman/MMFF94), atomic charge
• Not maintained: atom ID
• Bonds
• Maintained: bond type
• Not maintained: bond ID
• Substructures
• Maintained: substructure type and name
• Not maintained: substructure ID
• Sets
• Any sets with identical names in the source and target area will be
combined into a single set when merged.
• Defined features
• Maintained under certain conditions: center of mass, centroid, plane,
and normal are merged if the dummy atoms that define them are
included in the merge operation. However, they are not merged if
features of identical names are found in the source and target area.
• Not maintained: extension point, UNITY features and attributes.
• Data structures used in force field calculations
• Maintained: Any defined constraint, but only if all atoms associated
with the constraint are merged. (Refer to the Force Field Manual.)
• Not maintained: force field periodic boundary conditions
• Data structures associated with systematic conformational search
• Not maintained: rotatable bond, anchor atom, ring closure

Unique Versus Non-Unique Atoms

Unique Atom: The following scenarios define a unique atom:

• If the coordinates and the atom types in both the source and the target
area are different, an atom is considered to be unique.
• If the coordinates in the source and the target area are the same, but the
atom types are different, an atom is considered to be unique.

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• If the atom types in the source and the target are the same, but the
coordinates are different, an atom is considered to be unique.
You can set the distance within which two atoms are considered identical and
whether to keep only unique atoms.

Non-unique Atom: An atom in the source area with the same atom type and
coordinates as an atom in the target area. See Example of Merging Non-Unique
Atoms below.

See Tailor subject MERGE to determine the fate of non-unique atoms.

Example of Merging Non-Unique Atoms

Normally there is nothing to merge if two atoms are not unique. There are some
cases however, where they may be merged.

Non-unique atoms from the source area may be merged into the target area
when both of the following conditions have been met:
• The non-unique atom in the source molecule area has a unique atom
attached to it.
• In the target molecule area there is no open valence on the atom corre-
sponding to the non-unique atom in the source molecule area.

The unique atom carries with it the non-unique atom to preserve the bonding
information.

1. Read in a methane molecule into M1 and into M2. Then change one of the
hydrogens to bromine.
! File > Get Fragment

! Type or select METHANE and press OK.

! File > Get Fragment

! Type or select METHANE and press OK.

! Use to set the screen mode to Half.

! Click any hydrogen atom in M1 (molecule on the right).

! Edit > Atom > Modify Atom Type

! In the Modify Atom Type dialog, select Br, activate Adjust Geometry,
then press OK.

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Relative to M2, only the bromine atom in M1 is unique. The carbon and
hydrogens are non-unique atoms.

2. Merging M1 into M2 will bring the unique bromine from the source area to the
target area (M2). The merge operation will also bring the non-unique carbon
connected to the bromine into the target area.

! Double-click any atom in M1 to select the whole molecule.

! Edit > Merge

! Select M2:methane and press OK.

3. M2 now contains 7 atoms. Label them by ID number.

! Click any atom in M2.

! Click and select Molecule > Atom ID.

4. List the contents of M2:

! Options > List > Atoms

! In the Atom Expression dialog, select M2 from the pull-down at the top
of the dialog.

! Press and press OK.

! Select BRIEF and press OK.

The console reports the following:

Molecule area M2 Atoms
Molecule Name: methane
Number of defined atoms: 7

id name substructure type x y z charge

-- ---- ------------ ---- - - - ------
1 C1 METHANE C.3 0.0000 0.0000 0.0000 0.000
2 H1 METHANE H -0.2694 -0.7900 0.7164 0.000
3 H2 METHANE H 0.9250 0.4950 0.3308 0.000
4 H3 METHANE H 0.1572 -0.4444 -0.9939 0.000
5 H4 METHANE H -0.8128 0.7394 -0.0533 0.000
6 BR1 METHANE Br -0.4747 -1.3919 1.2622 0.000
7 METHAN+ METHANE C.3 0.0000 0.0000 0.0000 0.000
Number of atoms selected for listing: 7

! When finished, use the icon to reset the screen mode to Full.

! > Delete Everything

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9.2.2 Join Two Atoms from Separate Molecules

Join two molecular fragments by adding a covalent bond between them. The
two specified atoms are eliminated by the join operation.

Menubar: Not accessible from the menubar.

Command: JOIN target_atom new_group_atom
• target_atom—Atom to replace with the group being
added.
• new_group_atom—Atom in the joining group that will
be discarded.

The length and type of the new bond are determined by the type of the atoms
being joined and are taken from a table of standard bond lengths and types.

The fragments being joined may be in the same or difference molecule areas. In
the latter case, the atoms to be joined are copied into the target atom’s molecule
area and then the bond formed.

Additional Information:
• Add Bonds Manually on page 148 to connect two atoms
• Merge Atoms from Separate Molecules on page 112
• Tailor subject JOIN to customize the parameters for joining

9.2.3 Fuse Atom Pairs from Separate Molecules

Although this operation is most often done to fuse two rings, the two structures
do not have to be cyclic. At least two atoms must be selected in each molecule;
more atoms help direct fusion of non planar bonds.

Menubar: Not accessible from the menubar.

Command: FUSE {atom_pairs}
Terminate the input list with the end-loop character (|).

SYBYL places the fused structure in the molecule area of the first atom of each
pair. Coordinates of atoms used for the fusion are taken from the first molecule.
The bonds directly connecting fusion atoms in each molecule are discarded. An
attempt is made to retain all other bonds in both molecules. If the atomic
valence of the fusion atom is exceeded, any Hs attached to fusing atoms are
discarded and the fusion rechecked. If the operation still fails, an error is
reported and the command is terminated. You must then discard enough atoms
to make the fusion valid. If the operation succeeds, hydrogens are replaced to
fill valences of atoms from which they were removed.

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If you specify fusion of two molecules across an aromatic or double bond by

selecting only two atoms, alignment of resulting fragments is unambiguous. If,
however, fusion across a single bond involving tetrahedral atoms is specified by
two atoms, ambiguity arises. The program attempts to select the alternative
which results in the best fusion geometry. If you prefer another alternative
fusion geometry, select three or more atoms to unambiguously establish the
geometry.

Spiro fusions cannot be specified by selecting a single atom pair. They can be
specified by adding Hs and indicating the fusion of an internal bond in one
molecule with the bond involving the H atom.

Additional Information:
• Ring Fusion Tutorial on page 117
• Tailor subject FUSE to customize the handling of hydrogens during
fusion

9.2.4 Ring Fusion Tutorial

The following tutorial illustrates several examples of fusions:
• Fuse Two Planar Bonds
• Fuse Two Rings to Build a Spiro System
• Fuse Two Non Planar Bonds
• Fuse A Planar Bond With A Non Planar Bond

A Matter of Time: This tutorial requires about 3 minutes of personal time.

Set Up

1. It is always a good idea to clear the screen and reset the display before starting.

! > Delete Everything

! Click to reset all rotations and translations.

Fuse Two Planar Bonds

The fusion of two planar systems requires only two pair of atoms. In this
example, furan (M1) is fused to pyridine (M2) and the resulting model appears
in M2.

2. Read in the two fragments, color them by atom type, and label both structures.

! File > Get Fragment

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! Select FURAN and press OK.

! File > Get Fragment

! Select PYRIDINE and press OK.

3. Set the screen mode to display the molecules side by side.

! Use to set the screen mode to Half.

4. Label the atoms by ID numbers.

! Use to label the Molecules by Atom ID.

5. Fuse the two structures.

! In the console, type: fuse

! Click atom 6 in pyridine then atom 2 in furan to form the first pair.

! Click atom 5 in pyridine then atom 3 in furan to form another pair.

! In the Select Atom dialog, press End.

Furan is fused to pyridine. The molecule whose atom was selected first
(pyridine) to perform the ring fusion is updated.

Fuse Two Rings to Build a Spiro System

You can specify a spiro fusion by first selecting the two atoms that become the
spiro center. The second pair involves a ring atom in one molecule and a
hydrogen in the other.

1. Clear the SYBYL screen.

! > Delete Everything

2. Read in the two molecules.

! File > Get Fragment

! Select 4H-PYRAN and press OK.

! File > Get Fragment

! Select PIPERIDINE and press OK.

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3. Label the atoms by ID numbers.

! Use to label the Molecules by Atom ID.

4. Fuse the two rings.

! In the console, type: fuse

! Click atom 4 in piperidine, and then atom 4 in 4H-pyran to form the

first pair.
! Click atom 12 in piperidine, and then atom 5 in 4H-pyran to form
another pair.
! In the Select Atom dialog, press End.

The two rings are fused with a spiro center; the resulting model appears in M2.

Fuse Two Non Planar Bonds

In the following steps, you will fuse tetrahydropyran (M1) to piperidine. Several
methods are used by providing:
• Two pair of atoms (result in M2),
• Three pair of atoms (result in M3),
• Four pair of atoms (result in M4).

1. Clear the SYBYL screen.

! > Delete Everything

2. Load the molecules and label the atoms.

! File > Get Fragment

! Select TETRAHYDROPYRAN and press OK.

! File > Get Fragment

! Select PIPERIDINE and press OK.

! Use to set the screen mode to Quartered.

! Double-click any atom in piperidine to select the entire molecule.

! Click , and press OK to accept M3:<empty> as the destination.

! Click , and press OK to accept M4:<empty> as the destination.

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! Click away from all molecules to clear the selection.

! Use to label the Molecules by Atom ID.

3. Use two pair of atoms to fuse two non planar bonds. SYBYL resolves the
ambiguity automatically by selecting the alternative which gives rise to the best
fusion geometry. The results are displayed in M2.

! In the console, type: fuse

! Click atom 6 in piperidine (in M2), and then atom 2 in tetrahydropyran

to form the first pair.
! Click atom 5 in piperidine (in M2), and then atom 3 in tetrahydropyran
to form another pair.
! In the Select Atom dialog, press End.

Two non planar bonds are fused. The resulting model with extraneous
hydrogens appears in M2, showing that the selection of two atom pairs was
insufficient for this type of fusion.

4. Use three pair of atoms to fuse two non planar bonds. As in the previous steps,
SYBYL automatically resolves the ambiguity. The results are displayed in M3.

! In the console, type: fuse

! Click atom 6 in piperidine (M3), and then atom 2 in tetrahydropyran

(M1) to form the first pair.
! Click atom 5 in piperidine (M3), and then atom 3 in tetrahydropyran
(M1) to form a pair.
! Click atom 16 in piperidine (M3), and then atom 1 in tetrahydropyran
(M1) to form a pair.
! In the Select Atom dialog, press End.

Two non planar bonds are fused; the resulting model appears in M3.

5. Use four pair of atoms to fuse two non planar bonds. The results of the fusion
are displayed in M4.

Manual fitting of the two bonds to be fused reveals that the torsional angles of
the four atoms involved are 60° in piperidine and -60° in tetrahydropyran. In
order to produce a geometry better suited for the cis fusion you want to perform,
tetrahydrofuran is inverted first.

! Edit > Chirality > Invert

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! Select M1:tetrayhydropyran from the pull-down.

! Press the icon and press OK.

! Clear the atom selection.

! In the console, type: fuse

! Click atom 6 in piperidine (M4), and then atom 2 in tetrahydropyran

(M1) to form the first pair.
! Click atom 5 in piperidine (M4), and then atom 3 in tetrahydropyran
(M1) to form a pair.
! Click atom 16 in piperidine (M4), and then atom 1 in tetrahydropyran
(M1) to form a pair.
! Click atom 15 in piperidine (M4), and then atom 4 in tetrahydropyran
(M1) to form a pair.
! In the Select Atom dialog, press End.

Two non planar bonds are fused; the resulting model appears in M4.

Fuse A Planar Bond With A Non Planar Bond

1. Load the molecules and label the atoms.

! > Delete Everything

! File > Get Fragment

! Select HEXAHYDROAZEPINE and press OK.

! File > Get Fragment

! Select BENZENE and press OK.

! Use to set the screen mode to Half.

! Use to label the Molecules by Atom ID.

2. Fuse benzene (M2) to hexahydroazepine (M1) to form a model in M1.

! In the console, type: fuse

! Click atom 5 in hexahydroazepine (M1), and then atom 1 in benzene

(M2) to form the first pair.

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! Click atom 4 in hexahydroazepine (M1), and then atom 2 in benzene

(M2) to form a pair.
! In the Select Atom dialog, press End.

The planar bond is fused with a non planar bond. Notice the poor quality of the
geometry at the ring fusion and the fact that extraneous hydrogens are left over
from the hexahydroazepine. Clean up and minimization are necessary before
this model could be used.

The best strategy to assure the quality of the fusion and reduce the need for
minimization is to make sure that the geometry of the bonds to be fused is
identical in both molecules before the fusion occurs.

3. This concludes the Ring Fusion Tutorial. Clear and reset the screen.

! > Delete Everything

! Click to reset all rotations and translations.

! Use to reset the screen mode to Full.

9.2.5 Average Multiple Conformations

Starting with multiple conformations of the same structure, create another
conformation where:
• The coordinates of every atom are the average of the X, Y, Z coordinates
of the corresponding atoms in the selected molecules.
• All other aspects of the molecule (bonds, substructures, features, etc.)
are taken (arbitrarily) from one of the selected molecules.

Menubar: Not accessible from the menubar.

Command: AVERAGE_MOL mol_expr target_mol
• mol_expr—Expression indicating the location of
existing molecules. Empty molecule areas are ignored.
• target_mol—Area in which to place the new molecule.

If the selected molecules do not all contain the same number of atoms, an error
message is displayed and no molecule is created. Make sure that all other
aspects of the molecules are consistent (bonds, substructures, etc.).

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Delete a Molecule

9.3 Delete a Molecule

Delete the specified molecule(s).

Menubar: Edit > Delete > Molecules

then specify the molecule(s) to delete.
Or select atom(s) in one or more molecules then
Edit > Delete > Selected Molecules
Toolbar Icon: Click the icon’s arrow and select Molecules
then select in the list of molecule(s).
Or select atom(s) in one or more molecules then click
the icon’s arrow > Selected Molecules.
Command: ZAP mol_expr

Background images, such as MOLCAD surfaces, associated with the deleted

molecules are removed from the screen as well.

How to delete a UNITY query that does not contain any atoms?

Menubar: Edit > Delete > Molecules then select the query in
the list of molecule(s).
Toolbar icon: Click the icon’s arrow and select Molecules
then select the query in the list of molecule(s).
Command: ZAP mol_area

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Name or Rename a Molecule

9.4 Name or Rename a Molecule

Molecule names can be arbitrary long and complex, containing any characters.
However, the following is recommended. Use only alphanumeric characters and
the underscore.

If molecule names are to be manipulated in SPL avoid special characters and

spaces.

Edit > Molecule • At least one atom must have been pre-selected.
> Name • If atoms were selected in multiple molecule areas
you will be prompted to specify which molecule
area contains the molecule to be (re)named.
• Before renaming a UNITY query that does not
contain any atom you must select it via Selection
> Select Molecules. This will enable the Edit >
Molecule menu item.
Atom right-click • If the clicked-on atom was not selected only the
> Rename Mole- molecule containing the clicked-on atom is
cule (re)named.
• If the clicked-on atom was selected and atoms were
selected in multiple molecule areas you will be
prompted to specify which molecule area contains
the molecule to be (re)named.
• UNITY queries that do not contain any atoms
cannot be renamed in this manner.
MODIFY MOLE- • mol_area—Area containing molecule to modify.
CULE NAME • name—Name to identify molecule.
mol_area name

How to change the name of a UNITY query that does not contain any atoms?
Changing the name of a molecule via Edit > Molecule > Name menu requires
that at least one atom in the molecule be selected. However, a UNITY query
that does not contain any atoms cannot be selected by clicking with the mouse
on any of its features. Pre-selection of the molecule must be done via the
Selection menu.

Menubar/Toolbar: Selection > Select Molecules

then Edit > Molecule > Name.
Command: MODIFY MOLECULE NAME mol_area name

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Chirality: Determine and Modify

9.5 Chirality: Determine and Modify

9.5.1 Determine Chirality
Both the chirality of an atom and the cis-trans isomerism about a double bond
can be determined by using a set of rules developed by Cahn, Ingold and Prelog
and adopted by IUPAC (See J. Org. Chem., 35, 9, 2849, (1970)). These rules
govern the sequencing of substituents about the chiral atom or double bond.
Once the substituents are assigned a priority, simple geometric algorithms
determine which type of isomerism is present. These same rules are used to
determine the prochirality of an atom.

Menubar: Edit > Chirality > Find

Command: CHIRAL
Options: • RS atom_expr—Determine R or S chirality of the
specified atoms.
• ZE bond_expr—Determine Z or E isomerism about the
specified double bonds.
• PRO_RS atom_expr—Determine PRO-R or PRO-S
chirality of the specified atoms.
• MARK_RS atom_expr—Determine R or S chirality of the
specified atoms and set the atom chirality attribute.
• MARK_ZE bond_expr—Determine Z or E isomerism
about the specified double bonds and set the bond
stereo attribute.

Any unfilled valences are assumed to be occupied by hydrogens.

The system determines the RS isomerism of an atom by positioning a three-

dimensional representation of the atom so that the lowest group in the sequence
is oriented away from the viewer. If the remaining substituents are arranged in a
clockwise manner by priority, the center is designated R, otherwise it is S.

ZE isomerism about a double bond is a more general designation than cis-trans;

it is determined by examining the bond’s substituents and sequencing them in
the manner prescribed by IUPAC (atomic number is the first criterion) which
encompasses the Cahn/Ingold/Prelog sequencing rules. The special relationship
between the higher priority substituent on each end of the double bond is
examined relative to a reference plane, which includes the two double bonded
atoms, and drawn perpendicular to the plane of the four substituents. If the two
higher priority substituents lie on the same side of this reference plane, the
isomerism is denoted as Z; if they lie on opposite side, it is E.

The built-in set {CHIRAL} determines only RS isomerism.

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Chirality attributes that have been set for atoms (MARK_RS) and bonds
(MARK_ZE) are visible in SLN-based 2D representations of the molecules, such
as via the SLN 2D Viewer. They are also used by the expression generator
%sln() when converting a SYBYL molecule to an SLN string (see the SLN
Manual for details).

Additional Information:
• SLN 2D Viewer (in the Graphics Manual)
• Delete Stereo Atom Attribute on page 127
• Delete Stereo Bond Attribute on page 127
• Delete Atom Attributes on page 140

9.5.2 Invert Chirality

Menubar: Edit > Chirality > Invert

Command: INVERT atom_expr

If all atoms in the molecule are to be inverted, the entire molecule is inverted by
reflecting the X-coordinate through the YZ plane. Otherwise, each individual
tetrahedral atom is inverted by exchanging two substituents. Note that non-
chiral centers may also be inverted.

Atoms at ring fusions cannot be inverted individually, but only as part of the
inversion of the whole molecule.

No chirality determination is done before or after the inversion. A message is

issued only if a selected center cannot be inverted due to a ring fusion. A count
of the number of tetrahedral centers successfully inverted is given.

If a molecule includes atom chirality attributes, these attributes are inverted as

well as the coordinates of the chosen atoms. Atom chirality attributes are set
either by the CHIRAL MARK_RS command or by using the expression generator
%sln_to_mol() to convert an SLN string to a SYBYL molecule.

9.5.3 Reflect Atoms Through a Plane

Menubar: Edit > Chirality > Reflect through Plane

Command: REFLECT atom_expr plane_name
• atom_expr—Atoms to reflect through the plane.
• plane_name—Name of plane through which the
reflection is performed.

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The plane must be defined on the molecule. Any arbitrary atoms may be
reflected through the plane. Examine the resulting bonding geometry carefully,
since the program pays no attention to the geometrical arrangement during this
operation.

Additional Information:
Define a Plane on page 163

9.5.4 Delete Stereo Atom Attribute

Menubar: Not accessible from the menubar.

Command: REMOVE STEREO_ATOM_ATTR expression

9.5.5 Delete Stereo Bond Attribute

Menubar: Not accessible from the menubar.

Command: REMOVE STEREO_BOND_ATTR expression

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9. Molecules: Build, Delete, Modify
Modify Molecule Attributes

9.6 Modify Molecule Attributes

9.6.1 Center of Rotation
Designate the atom(s) at the center of rotation when the mouse focus is set to
this molecule.

MODIFY MOLECULE CENTER_OF_ROTATION mol_area atom_expr

• mol_area—Molecule area containing molecule.
• atom_expr—Atom(s) to use as center of rotation.

Additional Information:
• Mouse Focus icon (in the SYBYL Reference Guide) to designate a
single object
• Center and Scale (in the Graphics Manual) to view the molecule in the
center of the screen without affecting its coordinates
• CENTER (in the Graphics Manual) to translates the molecule so that this
position becomes the origin of the molecule coordinate system

9.6.2 Molecule Name

See Name or Rename a Molecule on page 124.

9.6.3 Molecule Type

A molecule’s type provides the proper context for many operations, such as
selecting the sidechain atoms in a protein. Use the following command a
molecule read in from external source does not contain this information.

MODIFY MOLECULE TYPE mol_area type

• mol_area—Area(s) containing molecule(s) to modify.
• type—NUCLEIC_ACID_MOLECULE, SACCHARIDE_MOLECULE, PROTEIN,
SMALL_MOLECULE, MACRO_MOLECULE.

9.6.4 Molecule Root Atom

Molecules may have any number of independent fragments, each one composed
of at least a single substructure. Each fragment has one of its substructures
recorded in the molecule header, i.e., the “root” of the fragment “tree”.

MODIFY MOLECULE ROOT mol_area substr_sel comment

• mol_area—Area containing the molecule to modify.

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 9. Molecules: Build, Delete, Modify
Modify Molecule Attributes

• substructure_sel—Substructure to be the root of the molecule tree.

• comment—Comment to store with the new root.

9.6.5 Comment Associated with a Molecule

MODIFY MOLECULE COMMENT area comment
• area—Area(s) containing molecule(s) to modify.
• comment—Descriptive string, may contain any characters and be of
arbitrary length. Enclose the string in double quotes when entering
spaces or special characters.

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 10. Substructures: Delete, Modify

A substructure is a molecular fragment, a functional group, a residue in a

biopolymer, or the ligand in a protein-ligand complex.
• Delete Substructures on page 132
• Modify Substructures on page 133
• Modify a Substructure’s Name on page 133
• Modify a Substructure’s Root Atom on page 133
• Modify a Substructure’s Type on page 134
• Create/Modify a Substructure’s Comment on page 134

Additional Information:
• Definitions of SYBYL Objects on page 170
• Label in the Graphics Manual

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10. Substructures: Delete, Modify
Delete Substructures

10.1 Delete Substructures

Menubar: Select the substructure(s) to be deleted, then

Edit > Delete > Selected or Selected Atoms
Toolbar Icon: Click to delete the current selection.
Command: REMOVE SUBSTRUCTURE expression
• expression—Substructure expression indicating
substructure(s) to delete.

Additional Information:
• Label in the Graphics Manual
• Modify Substructures on page 133

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 10. Substructures: Delete, Modify
Modify Substructures

10.2 Modify Substructures

Substructure modification is not accessible from the menubar.

10.2.1 Modify a Substructure’s Name

MODIFY SUBSTRUCTURE NAME substructure_expr {mode name}
• substructure_expr—Substructures to modify.
• mode:
APPEND_AUTO—Single string is supplied and concatenated with selected
substructure’s current name.
QUERY—Name for each selected substructure is entered. Each selected
substructure is highlighted as you are prompted for its name.
SEQUENTIAL_AUTO—Element type name is concatenated with
substructure ID number.
• name—Name or fragment thereof to associate with the substructure in
all but SEQUENTIAL_AUTO mode. First character must be alphabetic and
may contain alphabetic, numeric, and the apostrophe.

To rename substructures (residues) in a biopolymer, use Biopolymer >

Prepare Structure > Renumber Sequence.

Additional Information:
Label in the Graphics Manual

10.2.2 Modify a Substructure’s Root Atom

MODIFY SUBSTRUCTURE ROOT substructure_expr {atom_sel}
• substructure_expr—Substructures to modify.
• atom_sel—Atom to be the root of each of the selected substructures.

Substructures are composed of connected atoms forming a “graph” structure.

The graph is traversed from the “root” to all other atoms in the substructure. All
bonds within the substructures are ordered such that when traversed from origin
to terminus, they are directed away from the root. This command alters the root
of the substructure and re-orders the graph. The root atom of a biopolymer
substructure is taken from the dictionary.

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10. Substructures: Delete, Modify
Modify Substructures

10.2.3 Modify a Substructure’s Type

MODIFY SUBSTRUCTURE TYPE substructure_expr {type}
• substructure_expr—Substructures to modify.
• type—DOMAIN, GROUP, PERMANENT, RESIDUE, TEMPORARY.

All types that are not temporary are permanent. Only RESIDUE has any special
meaning. It is used extensively in the manipulation of biopolymers where it is
synonymous with monomer. Generally you should not alter the substructure
types; they are managed by the system.

10.2.4 Create/Modify a Substructure’s Comment

MODIFY SUBSTRUCTURE COMMENT substructure_expr {comment}
• substructure_expr—Substructures to modify.
• comment—Descriptive string. It may contain any characters and be of
arbitrary length. Use double quotes when entering spaces or special
characters via command line.

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 11. Atoms: Add, Delete, Modify

This section describes how to perform the following operations.

• Add Atoms on page 136
• Add an Atom to an Existing Structure on page 136
• Add a Standalone Atom on page 136
• Add a Chain of Atoms of the Same Type on page 137
• Add Pseudo-atoms (Centroids) on page 137
• Add Hydrogens on page 138
• Fill Empty Valences with any Atom Type on page 138
• Delete Atoms or Atom Attributes on page 139
• Delete Atoms on page 139
• Delete All Hydrogens on page 140
• Delete a Connected Group of Atoms on page 140
• Delete Atom Attributes on page 140
• Modify Atoms on page 141
• Modify SYBYL Atom Types on page 141
• Modify Atom Name on page 144
• Modify Atom Charge on page 144
• Modify and Update Coordinates on page 145
• Renumber Atoms on page 145

Additional Information in the Graphics Manual:

• Label Selected Atoms
• Color Schemes
• Atom Rendering

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11. Atoms: Add, Delete, Modify
Add Atoms

11.1 Add Atoms

11.1.1 Add an Atom to an Existing Structure

Menubar: Edit > Atom > Add Connected Atom

Command: ADD ATOM attachment_atom type
• attachment_atom—Atom to which new one is bonded.
• type—New atom’s chemical type and hybridization.
(Type “?” at prompt to list available atom types.)

SYBYL automatically determines the coordinates, based on bond length and

bond angle data from parameter tables.

11.1.2 Add a Standalone Atom

Menubar: Edit > Atom > Add Standalone Atom

Command: ADD RAWATOM mol_area name type x y z
• mol_area—Area to receive new atom.
• name—Name for new atom (must start with an alpha-
betic character and contain only alphabetic characters,
digits, and/or the special symbols dollar sign ($), under-
score (_), or apostrophe (')).
• type—Chemical type and hybridization of atom. (Type
“?” at prompt to list available atom types.)
• x, y, z—Coordinates of atom.

Position the atom by specifying coordinates or by using the mouse.

136 SYBYL Basics SYBYL-X 2.1

 11. Atoms: Add, Delete, Modify
Add Atoms

11.1.3 Add a Chain of Atoms of the Same Type

Menubar: Edit > Atom > Add Chain of Atoms

Command: ADD CHAIN ATTACH | REPLACE [atom] type
length
• ATTACH—Add new chain to specified atom with appro-
priate geometry.
• REPLACE—Remove specified atom and add new chain
in its place, with ideal geometry (useful when
hydrogens are present).
• atom—Atom for attachment or to replace.
• type—Chemical type and hybridization of atoms in
chain. (Type “?” at prompt to list available atom types.)
• length—Length of chain to create, may vary from 1
upward (no upper limit). “1” is equivalent to the ADD
ATOM command.

SYBYL attaches chains to the existing structure with ideal geometry. SYBYL
determines the coordinates of all atoms from the parameter tables.

11.1.4 Add Pseudo-atoms (Centroids)

Pseudo-atoms (centroids) are added to prochiral, methyl, and phenyl ring
groups. They are often used for defining constraints to the prochiral, methyl, or
aromatic protons. Constraints are needed when you do not have stereospecific
resonance assignments for prochiral atoms (or methyl pairs, such as in leucine
and valine), or when fast motions are present (such as methyl rotors and
aromatic ring flipping).

Menubar: Edit > Atom > Add Pseudo-atoms

Command: ADD_PSEUDOATOMS mol_area

The dummy atom’s name at the centroid position is defined according to the
nomenclature first presented in Kurt Wüthrich, NMR of Proteins and Nucleic
Acids, J. Wiley and Sons, 1986. For example, the beta methyl group on alanine
is named “QB”.

The algorithm identifies appropriate atom sets, independently of the

substructure and atom names. For example, any pair of protons bonded to a
“heavy” atom, and that are not part of methyl groups, will have a pseudo-atom
added between them.

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11. Atoms: Add, Delete, Modify
Add Atoms

11.1.5 Add Hydrogens

Fill all empty valences with hydrogens. If the molecule is a protein, nucleic
acid, or saccharide, the Biopolymer functionality, BIOPOLYMER ADDH, is
exercised first. See License Requirements for SYBYL Basics on page 9.

Hydrogens added to invisible atoms are automatically made invisible.

Menubar: Edit > Hydrogens > Add All Hydrogens

Edit > Hydrogens > Add Polar Hydrogens
Edit > Hydrogens > Add Non-Polar Hydrogens
Adding hydrogens works on whole molecule areas, affect-
ing only those containing selected atoms or all of them is
nothing is selected.
The {POSSIBLE_HBOND} built-in set is used to identify
polar hydrogens.
Toolbar Icon: Add all hydrogens to molecule areas containing
selected atoms or to all of them if nothing is selected.
Command: FILLVALENCE atom_expr H
• atom_expr—Atoms to have empty valences filled with
hydrogens.

SYBYL sets bond lengths and angles to standard values determined from the
parameter file (described in the Force Field Manual).

Hydrogens, when added, acquire the rendering mode of the atoms they are
attached to.

11.1.6 Fill Empty Valences with any Atom Type

Menubar: Not accessible from the menubar.

Command: FILLVALENCE atom_expr atom_type
• atom_expr—Atoms to have empty valences filled.
• atom_type—Mnemonic type of atom to use in filling
valences.

SYBYL sets bond lengths and angles to standard values determined from the
parameter file.

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 11. Atoms: Add, Delete, Modify
Delete Atoms or Atom Attributes

11.2 Delete Atoms or Atom Attributes

11.2.1 Delete Atoms
Delete the specified atoms. Menubar and toolbar require pre-selection of atoms.

When using the graphical interface, invisible hydrogens connected to the

deleted atoms are also deleted.

Menubar: Select atom(s) in one or more molecules then

Edit > Delete > Selected Atoms.
The selected atoms and any invisible hydrogens con-
nected to them are deleted.
Toolbar Icon: Select atom(s) in one or more molecules then click the
icon’s arrow and select Selected Atoms.
The selected atoms and any invisible hydrogens con-
nected to them are deleted.
Atom Right-Click: • > Delete Atom—If the clicked-on atom is not
selected, only that atom is deleted along with any
invisible hydrogens connected to it.
• > Delete Selected Atoms—If the clicked-on
atom is selected, all selected atoms, regardless of
molecule area, are deleted along with any invisible
hydrogens connected to them.
Command: REMOVE ATOM atom_expr
Issue this command for each molecule in which atoms
must be deleted, making sure to include the appropriate
molecule area within the atom expression.
See How to Specify an Atom Expression (in the SPL
Manual).

Deleting atoms also removes all bonds involving the deleted atom(s) and any
features (normal, plane, constraint) attached to them. SYBYL renumbers atoms
and bonds to reflect the removal of objects from the molecular description. If a
deleted atom was a member of a static set, the set membership is updated.
Deleting all atoms is equivalent to deleting the molecule.

Unless an entire molecule is deleted, its associated background images, such as

MOLCAD surfaces, remain on the screen.

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11. Atoms: Add, Delete, Modify
Delete Atoms or Atom Attributes

11.2.2 Delete All Hydrogens

Edit > Hydrogens > Delete All Hydrogens

Deleting all hydrogens works on whole molecule areas, affecting only those
containing selected atoms or all of them is nothing is selected.

11.2.3 Delete a Connected Group of Atoms

Remove a portion of a molecule by specifying two bonded atoms:

Menubar: Not accessible from the menubar.

Command: SPLIT origin_atom target_atom

The bond between the specified atoms is deleted along with all atoms on the
target side of that bond.

Note: You can not use this functionality if the indicated bond is in a ring. You
must first break the ring by removing a bond or an atom.

11.2.4 Delete Atom Attributes

Atom attributes are used in the 2D SLN representation of a molecule to convey
information about stereochemistry and atomic charge. They are stored in Mol2
and SLN files.

Attributes can be removed from one or more atoms without deleting the atom
itself.

Command: REMOVE ALL_ATOM_ATTRS atom_expr

Additional Information:
• Determine Chirality on page 125
• Modify Atom Charge on page 144
• The SLN 2D Viewer in the Graphics Manual

140 SYBYL Basics SYBYL-X 2.1

 11. Atoms: Add, Delete, Modify
Modify Atoms

11.3 Modify Atoms

11.3.1 Modify SYBYL Atom Types
Modify the SYBYL atom type of one or more atoms. When specified via the
menubar, all selected atoms are changed to the same new atom type.

Menubar: Select any number of atoms in any number of molecules

then
Edit > Atom > Modify Type
In the dialog, specify the new atom type for the selected
atom(s) and indicate whether to adjust the geometry of
any associated acyclic bond(s).
Command (type MODIFY ATOM ONLY_TYPE atom_expr {type}
only): Prompts for the new atom type for each specified atom.
The geometry around atoms or atom names is not
changed.
Command (type MODIFY ATOM TYPE atom_expr {type}
and geometry): Prompts for the new atom type for each specified atom.
The lengths of associated acyclic bond(s) are also
adjusted.

The types of associated bonds are modified if necessary to fit the modified atom
types. If a bond’s type is ambiguous (i.e., there is more than one possible bond
type to connect the two atom types) or unknown, you will be prompted in the
console.

The names of modified atoms are automatically updated by replacing the old
atomic symbol with the new one (e.g. modifying the type of a hydrogen named
H8 to be a fluorine automatically updates the atom’s name to F8). This behavior
is controlled by Tailor variable ATOM_TYPE FIX_NAMES.

Bond lengths and types are taken from $TA_ASCTABLES/BOND_LENGTHS

and BOND_TYPES.

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11. Atoms: Add, Delete, Modify
Modify Atoms

11.3.2 AMBER, Kollman, MMFF94 Atom Types

Licensing: See License Requirements for SYBYL Basics on page 9.

In addition to SYBYL atom types a molecule’s description may include

alternate atom types for use in energy calculations using non-Tripos force
fields. These atom types can come from two sources: the biopolymer dictionary
or user input.

Currently supported alternate atom type sets are:

• AMBER7 FF99 (AMBER7_FF99) force field, which is essentially
AMBER95 atom types with a few types added. A list of AMBER7 FF99
atom types is provided in the Force Field Manual.
• AMBER7 FF02 (AMBER7_FF02) force field, which is essentially
AMBER7 FF99 atom types with different charges and polarization
included. A list of AMBER7 FF99 atom types is provided in the Force
Field Manual.
• AMBER 95 (AMBER95_ALL) force field.
• Kollman all-atom (KOLL_ALL) and Kollman united-atom (KOLL_UNI)
force fields. A list of Kollman atom types is provided in the Force Field
Manual. Note: Alternate atom types must be defined for both KOLL_UNI
and KOLL_ALL force fields for energy setup to work. If the atom type is
defined for only one, the ENERGY, MAXIMIN2, and DYNAMICS SETUP
commands all fail with an error condition.
• MMFF94 force field. A list of MMFF94 atom types is provided in the
Force Field Manual.

Assign Alternate Atom Types Automatically

Refer to the Biopolymer Manual to:

• Assign AMBER, Kollman or MMFF94 atom types for use in force field
minimizations.
• Load charges associated with atom types.

Assign Alternate Atom Types Manually

MODIFY ATOM OTHER_TYPES set_name ASSIGN

SPECIFIC|UNKNOWN
• set_name—Set of alternate atom types: KOLL_ALL, KOLL_UNI,
AMBER7_FF02, AMBER7_FF99, AMBER95_ALL, or MMFF94.
• SPECIFIC—Specify atoms to assign types to. You are prompted for the
atom types, one at a time, as the atom is highlighted.

142 SYBYL Basics SYBYL-X 2.1

 11. Atoms: Add, Delete, Modify
Modify Atoms

• UNKNOWN—Prompts for atom types for each atom in molecule which

does not yet have an alternate atom type.

Assign Alternate Atom Types via the SLN Typer

MODIFY ATOM OTHER_TYPES set_name SLN_AUTO_ASSIGN

SPECIFIC|UNKNOWN
• set_name—Set of alternate atom types: KOLL_ALL, AMBER7_FF02,
AMBER7_FF99, AMBER95_ALL.
• SPECIFIC—Specify the atoms to assign types to.
• UNKNOWN—Prompts for atom types for each atom in molecule which
does not yet have an alternate atom type.

Unassign Alternate Atom Types

MODIFY ATOM OTHER_TYPES set_name UNASSIGN atom_expr

• set_name—Set of alternate atom types: KOLL_ALL, KOLL_UNI,
AMBER7_FF02, AMBER7_FF99, AMBER95_ALL, or MMFF94.

Label Alternate Atom Types

MODIFY ATOM OTHER_TYPES set_name LABEL mol_area

• set_name—Set of alternate atom types: KOLL_ALL, KOLL_UNI,
AMBER7_FF02, AMBER7_FF99, AMBER95_ALL, or MMFF94.

View > Label > Molecules > Atom Type

The menubar operation applies to pre-selected atoms or to all molecule areas
if no atoms were selected. See Label in the Graphics Manual.

Unlabel Alternate Atom Types

MODIFY ATOM OTHER_TYPES set_name UNLABEL mol_area

• set_name—Set of alternate atom types: KOLL_ALL, KOLL_UNI,
AMBER7_FF02, AMBER7_FF99, AMBER95_ALL, or MMFF94.

List Alternate Atom Types

MODIFY ATOM OTHER_TYPES set_name LIST

SPECIFIC|UNKNOWN|USER_ASSIGNED
• set_name—Set of alternate atom types: KOLL_ALL, KOLL_UNI,
AMBER7_FF02, AMBER7_FF99, AMBER95_ALL, or MMFF94.

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11. Atoms: Add, Delete, Modify
Modify Atoms

• SPECIFIC—List the alternate types of all specified atoms, including

their source (user-specified, or default—from macromol dictionary).
• UNKNOWN—List the names of all atoms with unknown alternate atom
types.
• USER_ASSIGNED—List the types of all atoms with user-assigned
alternate types.

User-assigned types are stored with the molecule and take precedence in force
field calculations over dictionary-supplied alternate atom types.

11.3.3 Modify Atom Name

Menubar: Select a single atom then

Edit > Atom > Rename
In the dialog, enter the atom’s new name.
Change Name: MODIFY ATOM NAME atom_expr
APPEND_AUTO|QUERY|SEQUENTIAL_AUTO
• APPEND_AUTO—Supply a single string to concate-
nated with the current name for each selected atom.
• QUERY—Prompts for the name for each selected
atom.
• SEQUENTIAL_AUTO—For each selected atom,
concatenate the atomic element with the atom ID
number to form the new name.

The first character of name must be alphabetic. All others must be alphabetic,
numeric, or an underscore. Spaces and all characters that follow a space are
ignored. Although names can be arbitrarily long, the recommended maximum
length of an atom name is 7 characters.

11.3.4 Modify Atom Charge

Assign formal charges to atoms for use in the SLN representation of a molecule.

Menubar: Select a single atom then

Edit > Atom > Set Charge
In the dialog, enter the atom’s charge.
Command: MODIFY ATOM CHARGE atom_expr {charge}
Prompts for the atomic charge for each specified atom.

Atomic charges that are specified this way are stored as atom attributes and
made visible in SLN-based 2D representations of the molecules, such as
obtained via the SLN 2D Viewer. They are also used by the expression generator
%sln() when converting a SYBYL molecule to an SLN string.

144 SYBYL Basics SYBYL-X 2.1

 11. Atoms: Add, Delete, Modify
Modify Atoms

Usage Note: The operation that computes atomic charges on an entire molecule
(Compute > Charges) ignores any charges that have been assigned to
individual atoms.

Additional Information:
• SLN 2D Viewer (in the Graphics Manual)
• Delete Atom Attributes on page 140

11.3.5 Modify and Update Coordinates

Menubar: Not accessible from the menubar.

Change Coordi- MODIFY ATOM COORDINATES atom_expr
nates: xyz_coord
Changes are not restricted by the bond length table nor
by atoms being in rings. Coordinates are unconditionally
altered.
Update Lone Pairs: MODIFY ATOM LONE_PAIR atom_expr
Lone pair positions may need to be updated after whole
or partial structural changes are made to the molecule,
such as minimizations. Geometry optimizations using
Tripos force field do not affect lone pair positions. Use
this command before defining an extension point if any
atoms involved are lone pairs.
Recalculate Exten- MODIFY ATOM SYBYL_POINTS atom_expr
sion Points/Lone Use if extension points/lone pairs become distorted dur-
Pairs: ing other calculations.

11.3.6 Renumber Atoms

Renumbering atoms imposes an arbitrary order on atoms in a molecule.

Usage Note: Label all atoms by ID numbers before proceeding with the renum-
bering.

Menubar: Not accessible from the menubar.

Command: RENUMBER origin_area target_area {atom_ID}
• origin_area—Area containing molecule to renumber.
• target_area—Area to receive renumbered molecule.
• atom_ID—For each position in the new numerical order
enter the old ID number.

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11. Atoms: Add, Delete, Modify
Modify Atoms

The renumbering operation can be terminated at any time. Atoms not specified
to be renumbered retain their relative order and are added to the molecule list
immediately behind atoms which were renumbered.

Renumbering atoms causes all defined features to be deleted from the molecule
because there is no automatic translation from the internal representation of the
feature definition to atom numbers. All other information about the molecule is
suitably transformed and restored after renumbering.

146 SYBYL Basics SYBYL-X 2.1

 12. Bonds: Add, Delete, Modify
• Add Bonds on page 148
• Add Bonds Manually on page 148
• Add Bonds Automatically on page 148
• Delete Bonds on page 150
• Delete Bond Attributes on page 150
• Modify a Bond Type on page 151

Additional Information:
• Label in the Graphics Manual
• Modify a Bond Length on page 157
• Adjust Bond Lengths and Angles to Match Standards on page 158

SYBYL-X 2.1 SYBYL Basics 147

12. Bonds: Add, Delete, Modify
Add Bonds

12.1 Add Bonds

12.1.1 Add Bonds Manually
Add bond(s) between designated atoms.

Menubar: Edit > Bond > Add Atom By Atom

Repeats adding bonds until End is selected.
Command: ADD BOND origin_atom target_atom
• origin_atom—Atom at beginning of bond.
• target_atom—Atom at end of bond.

The bond type of the new bond is set by the atom types at its endpoints. If there
is ambiguity regarding the bond type, a prompt asks for the resolution. Atomic
positions are not altered by adding a bond.

12.1.2 Add Bonds Automatically

Automatically adds a single bond between two atoms if the distance between
them is within an acceptable range.

Menubar: Edit > Bond > Add Quick Bonds

Command: QUICKBOND mol_area atom_expr
• mol_area—Molecule area containing the molecule.
• atom_expr—Atoms between which connectivities must
be identified.

SYBYL adds a bond between two atoms, A and B, if the distance between
them, DISTAB, is within acceptable range:

Ideal_Bond(1-Tol_Neg) < DistAB < Ideal_Bond (1+Tol_Pos) [EQ 1]

where:
• Ideal_Bond—Standard bond length between atom types A and B in
the bond length table.
• Tol_Neg—Tolerance used to determine low end of the distance
range. This Tailor variable has a default of 0.30.
• Tol_Pos—Tolerance used to determine high end of the distance
range. This Tailor variable has a default of 0.10.

The asymmetry of the acceptance window (Tol_Neg > Tol_Pos) allows for
alkynes (Ideal_Bond = ~1.15 Å) and certain short aromatic C-C bonds to be
recognized as bonds without making chemical oddities from non-covalent
intramolecular hydrogen bonding patterns.

148 SYBYL Basics SYBYL-X 2.1

 12. Bonds: Add, Delete, Modify
Add Bonds

By adding only single bonds, molecular connectivity can be determined with a

high degree of accuracy and minimum user intervention. Check all atom and
bond types within the specified atom expression before proceeding with calcula-
tions, where this information is relevant.

Additional Information:
• Join Two Atoms from Separate Molecules on page 116
• Tailor subject CONNECT to alter the characteristics of the connectivity
determination

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12. Bonds: Add, Delete, Modify
Delete Bonds

12.2 Delete Bonds

Menubar and toolbar do not require pre-selection, but will act on pre-selected
atoms by deleting the bond(s) between them.

Menubar: Edit > Delete > Bonds

Toolbar Icon: > Bonds
Command: REMOVE BOND bond_expr

Features (rotatable bonds) associated with the deleted bond are removed as well.
Bonds are renumbered to reflect the removal of objects from the molecular
description. If one of the two last atoms in a substructure is a biopolymer atom
(as defined in the macromol dictionary), SYBYL retains the root atom in the
substructure and the other atom in the substructure zero.

12.2.1 Delete Bond Attributes

Bond attributes are used in the 2D SLN representation of a molecule to convey
information about stereochemistry. They are stored in Mol2 and SLN files.

Attributes can be removed from one or more bonds without deleting the bonds
themselves.

Command: REMOVE ALL_BOND_ATTRS expression

Additional Information:
• Determine Chirality on page 125
• The SLN 2D Viewer in the Graphics Manual

150 SYBYL Basics SYBYL-X 2.1

 12. Bonds: Add, Delete, Modify
Modify a Bond Type

12.3 Modify a Bond Type

Menubar: Edit > Bond > Modify Type
Command: MODIFY BOND AUTO_TYPE|TYPE bond_expr
{type}
• AUTO_TYPE—Force the automatic determination
of bond type according to the types of the atoms
at each end of the bond. Only prompts for bonds
whose types are ambiguous.
• TYPE—Prompt for the type for each specified
bond.

No adjustment of parameters other than type is attempted for the selected bonds.

SYBYL bonds types are defined in $TA_ASCTABLES/BOND_TYPES (refer

to the Force Field Manual for information). Only one bond type can be assigned
to each bond.

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 13. Geometry: Measure, Modify, Define Features
• Geometric Measurements on page 154
• Intra-/Intermolecular Measurements on page 154
• Measure the Intramolecular Angle Between Planes on page 155
• Measurements Specific to UNITY Features on page 155
• List Coordinates, Distances, or Angles on page 156
• Modify Molecular Geometry on page 157
• Modify a Bond Length on page 157
• Modify a Bond Angle on page 157
• Modify a Torsion Angle on page 157
• Adjust Bond Lengths and Angles to Match Standards on page 158
• Scan Torsions to Reduce van der Waals Contacts on page 158
• Geometric Features: Define and Modify on page 159
• Center of Mass on page 159
• Define the Centroid of a Group of Atoms on page 160
• Define an Extension Point on page 161
• Define a Line on page 162
• Define a Plane on page 163
• Define the Normal to a Plane on page 164
• UNITY Query Features on page 166

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13. Geometry: Measure, Modify, Define Features
Geometric Measurements

13.1 Geometric Measurements

• Intra-/Intermolecular Measurements on page 154
• List Coordinates, Distances, or Angles on page 156
• Measure the Intramolecular Angle Between Planes on page 155
• Measurements Specific to UNITY Features on page 155

Additional Information:
• BIOPOLYMER MEASURE to measure omega and zeta angles
• Tailor variable GENERAL ANGLE_RANGE to specify how an angle range
should be displayed

13.1.1 Intra-/Intermolecular Measurements

Angles

Menubar: Compute > Measure > Angle

Command: MEASURE ANGLE {atom1 atom2 atom3}
Loops until you type the end-loop character (|).
UIMS2 Variable: MEASURE_ANGLE

Distance

Menubar: Compute > Measure > Distance

Command: MEASURE DISTANCE {atom1 atom2}
Loops until you type the end-loop character (|).
UIMS2 Variable: MEASURE_DISTANCE

Height of Atoms Above Plane

Menubar: Compute > Measure > Height Above Plane

Command: MEASURE HEIGHT atom_expr plane_name
• atom_expr—Atoms whose height is to be measured.
• plane_name—Name of plane, in default work area, to
use. Use LIST PLANE to find names of defined planes.
Note: Plane coordinates and plane normal lines are not
updated when you use FREEZE. Use EVALUATE PLANE
mol_area name, then EVALUATE NORMAL mol_area
name to update the plane and normal line.
UIMS2 Variable: MEASURE_HEIGHT

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 13. Geometry: Measure, Modify, Define Features
Geometric Measurements

Torsion Angles

Menubar: Compute > Measure > Torsion

Command: MEASURE TORSION {atom1 atom2 atom3 atom4}
Loops until you type the end-loop character (|).
UIMS2 Variable: MEASURE_TORSION

Additional Information:
List Coordinates, Distances, or Angles on page 156

13.1.2 Measure the Intramolecular Angle Between Planes

Compute the angle between two pre-defined planes and report a value between
0 and 90°.

Menubar: Compute > Measure > Plane Angle

Command: MEASURE PLANE_ANGLE mol_area plane_name1
plane_name2
Use LIST PLANE to find names of defined planes.
Note: Plane coordinates and plane normal lines are not
updated when you use FREEZE. Use EVALUATE PLANE
mol_area name, then EVALUATE NORMAL mol_area
name to update the plane and normal line.
UIMS2 Variable: MEASURE_PLANE_ANGLE

Refer to Define a Plane on page 163.

13.1.3 Measurements Specific to UNITY Features

MEASURE UNITY_MEASUREMENTS mol_area option

Option:

ANGLE atom1 atom2 atom3 Measure angle of atoms.

DISTANCE atom1, atom2 Measure distance between atoms.
HEIGHT atom_expr plane_name Measure height of atom above plane.
PLANE_ANGLE plane_name1 Measure angle between planes in
plane_name2 same work area.
TORSION atom1 atom2 atom3 Measure torsion angle of atoms.
atom4

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13. Geometry: Measure, Modify, Define Features
Geometric Measurements

13.1.4 List Coordinates, Distances, or Angles

Menubar: Compute > Measure > Topography

List Bond Angles TOPOGRAPHY ANGLES atom_expr
via Command: • atom_expr—Expression indicating angle(s). All
angles having the center atom in this atom
expression are listed
List Bond Lengths TOPOGRAPHY BOND_LENGTH atom_expr
via Command: • atom_expr—Expression indicating bond(s). All
bonds having either their origin or their target in
this expression are listed.
List Coordinates TOPOGRAPHY COORDINATES atom_expr
via Command: • atom_expr—Expression indicating atoms whose
coordinates are to be listed.
Coordinates listed by this command are affected by
rotations and translations applied to molecule on the
terminal. To list coordinates in memory, use the LIST
ATOMS command. Alternatively, cancel rotation/transla-
tion matrix using the reset feature on your terminal, or
FREEZE coordinates before issuing the TOPOGRAPHY
command.
List Non-bonded TOPOGRAPHY NON_BONDED_LENGTH atom_expr1
Distance via Com- atom_expr2
mand: Distances between every atom in atom_expr1 and every
atom in atom_expr2 are listed.
List Torsion TOPOGRAPHY TORSION_ANGLE bond_expr
Angles via Com- • bond_expr—Expression indicating torsion(s). All
mand: torsion angles having the center bond in this bond
expression are listed.

Additional Information:
• Record the Output from a Single Command on page 204
• Intra-/Intermolecular Measurements on page 154
• BIOPOLYMER MEASURE to conveniently measure omega and zeta angles
• BIOPOLYMER CHECK_GEOMETRY to report deviations from standard
geometry

156 SYBYL Basics SYBYL-X 2.1

 13. Geometry: Measure, Modify, Define Features
Modify Molecular Geometry

13.2 Modify Molecular Geometry

13.2.1 Modify a Bond Length
Change the length of the bond between two connected atoms.

Menubar: Edit > Bond > Modify Distance

Command: MODIFY DISTANCE atom1 atom2 value

When a bond’s length is changed the coordinates of the second atom and all
atoms attached to it are altered. If the bond is in a ring, an error is reported and
no alteration is made.

13.2.2 Modify a Bond Angle

Change the bond angle between three connected atoms.

Menubar: Edit > Bond > Modify Angle

Command: MODIFY ANGLE atom1 atom2 atom3 angle

When changing a bond angle the coordinates of last atom and all atoms attached
to it are altered. If the atoms are in a ring, an error is reported and no alteration
is made.

13.2.3 Modify a Torsion Angle

Change the torsion angle between four connected atoms.

Menubar: Edit > Bond > Modify Torsion

Command: MODIFY TORSION atom1 atom2 atom3 atom4
angle

When changing a torsion angle the coordinates of last atom and all atoms
attached to it are altered. If the atoms are in a ring, an error is reported and no
alteration is made.

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13. Geometry: Measure, Modify, Define Features
Modify Molecular Geometry

13.2.4 Adjust Bond Lengths and Angles to Match Standards

The Shaked algorithm iteratively loops through the selected atoms, adjusting
bond lengths and bond angles, to more closely match standard values stored in
the bond length and the Tripos force field bond angle tables.

Corrections are applied to coordinates to satisfy distance constraints:

L ij ≤ D ij ≤ U ij [EQ 2]

Where Lij is the lower bound for the distance (Dij) between atoms i and j, and
Uij is the upper bound. A delta of 0.05 is added to or subtracted from the value
obtained from the parameter tables to derive the upper and lower bounds,
respectively.

This operation is performed until either the maximum number of iterations

(100) is reached or convergence has occurred, that is, all constraints are met.
The algorithm fails when distance constraints are inconsistent or the input
structure is very different from the structure that obeys all distant constraints.

This algorithm is described by I. Haneef, Simon J. Talbot, and Peter G.

Stockley in J. Mol. Graphics, 7, 186-195 (1989).

Menubar: Edit > Clean-Up Molecule > Shake Bonds and

Angles
Acts on selected atoms in a single molecule area.
Command: SHAKED atom_expr

13.2.5 Scan Torsions to Reduce van der Waals Contacts

Menubar: Edit > Clean-up Molecule > Scan Torsions

Acts on selected bonds in a single molecule area.
Command: SCAN bond_expr

The specified torsion angles are scanned, through a full 360°, for positions
which relieve bad steric interactions. Only one bond at a time is altered. After a
position is found, that bond is removed from the set being considered. Scanning
continues until all interactions dependent upon these bonds are relieved or until
no progress is made from one iteration to the next.

Additional Information:
• Tailor subject SCAN to alter characteristics of the scan
• The following BIOPOLYMER subcommands: ADD_SIDECHAIN, CHANGE,
INSERT, JOIN, SET CONFORMATION

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 13. Geometry: Measure, Modify, Define Features
Geometric Features: Define and Modify

13.3 Geometric Features: Define and Modify

Geometric features are represented by dummy atoms defined from existing
atoms.
• Center of Mass on page 159
• Define the Centroid of a Group of Atoms on page 160
• Define an Extension Point on page 161
• Define a Line on page 162
• Define the Normal to a Plane on page 164
• Define a Plane on page 163
• UNITY Query Features on page 166

Note:
Whole or partial re-orientation (via Fit Atoms, Freeze Molecule, ORIENT,
geometrical modification or manipulation of rotatable bonds) after defining
centers of mass, centroids, extension points, normals, or planes renders the
feature invalid. Use the EVALUATE command to update the feature’s position.

Additional Information:
List Information About SYBYL Objects on page 175

13.3.1 Center of Mass

A centroid is a dummy atom at the center of a group of atoms. The center of
mass is a centroid with coordinates weighted by the atomic masses. When
defined, the dummy atom is added to the coordinate list and a feature in the
molecular description. The dummy atom is connected through a dummy bond to
the atom used in the calculation closest to its position. Dummy atoms have the
type Du and are colored magenta.

Define DEFINE CENTER_OF_MASS atom_expr name comment

• atom_expr—The atoms in a single molecule whose center
of mass will be computed.
• name—The name to give to the center of mass. Names
must start with an alphabetic character and may contain
digits and underscores.
• comment—A descriptive string associated with the center
of mass that may contain any characters and be of arbitrary
length. Enclose the string in double quotes when entering
spaces or special characters.

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13. Geometry: Measure, Modify, Define Features
Geometric Features: Define and Modify

Re-Evaluate: EVALUATE CENTER_OF_MASS mol_area name

• mol_area—Area(s) containing center(s) of mass to
evaluate.
• name—Name of center(s) of mass to evaluate. Enter a
question mark (?) to obtain a list. The expression may
include the wildcard character (*) (e.g., to remove both c1
and c2, enter c*, but the expression c1,c2 is not valid).
The new coordinates are computed and stored in the molecular
definition.
Show and VISUALIZE CENTER_OF_MASS mol_area name ON|OFF
Hide:
Remove: REMOVE CENTER_OF_MASS mol_area name

Note: Atomic weights correlate with the latest accepted figures from IUPAC
and NIST. For unstable atoms, the values for the most stable isotope are used.
• IUPAC: Pure Appl. Chem., Vol.75, No.8, pp 1107-1122, 2003.
• National Institutes of Standards and Technology (NIST)

For more information, see $TA_ROOT/sybylbase/tables/metals/

ATOM_DEF.

13.3.2 Define the Centroid of a Group of Atoms

A centroid is a dummy atom at the center of a group of atoms. When defined, it
is added to the coordinate list and a feature in the molecular description. The
dummy atom is connected through a dummy bond to the atom used in the calcu-
lation closest to its position. Dummy atoms have the type Du and are colored
magenta. (See Tailor subject CENTROID to alter the characteristics of the
centroid.)

Define via the Edit > Centroid > Define

Menubar:
Define via Com- DEFINE CENTROID atom_expr name comment
mand: • atom_expr—The atoms in a single molecule whose
centroid will be computed.
• name—The name to give to the centroid. Names must
start with an alphabetic character and may contain
digits and underscores.
• comment—A descriptive string associated with the
centroid that may contain any characters and be of
arbitrary length. Enclose the string in double quotes
when entering spaces or special characters.

160 SYBYL Basics SYBYL-X 2.1

 13. Geometry: Measure, Modify, Define Features
Geometric Features: Define and Modify

Re-Evaluate: EVALUATE CENTROID mol_area name

• mol_area—Area(s) containing centroid(s) to evaluate.
• name—Name of centroid(s) to evaluate. Enter a
question mark (?) to list names. Expression may
include the wildcard character (*) (e.g., to remove both
c1 and c2, enter c*, but the expression c1,c2 is not
valid).
The new coordinates are computed and stored in the
molecular definition.
Show and Hide: VISUALIZE CENTROID mol_area name ON|OFF
Remove via the Edit > Centroid > Delete
Menubar:
Remove via REMOVE CENTROID mol_area name
Command: Any features (plane, normal, constraint) attached to that
centroid are removed as well.

13.3.3 Define an Extension Point

An extension point is a dummy atom connected to the molecule that can be used
as a place holder. The extension point can represent a ligand atom or a hydrogen
bond partner. It is added as a dummy atom in the coordinate list and a feature in
the molecular description. It is connected through a dummy bond to the first
atom that defines it.

Define DEFINE EXTENSION_POINT atom1 atom2 atom3 dist

ang tors name comment
• atom1, atom2, atom3—IDs of atoms defining extension
point. If any are lone pairs, use the command MODIFY
ATOM LONE_PAIR first.
• dist—Distance from atom1 to the extension point.
• ang—Angle formed by atom 1, atom 2, and the extension
point.
• tors—Torsion angle formed by atom1, atom2, atom3, and
the extension point.
• name—The name to give to the extension point. Names
must start with an alphabetic character and may contain
digits and underscores.
• comment—A descriptive string associated with the
extension point that may contain any characters and be of
arbitrary length. Enclose the string in double quotes when
entering spaces or special characters.

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13. Geometry: Measure, Modify, Define Features
Geometric Features: Define and Modify

Re-Evaluate: EVALUATE EXTENSION_POINT mol_area name

• mol_area—Area(s) containing point(s) to evaluate.
• name—Name of point(s) to evaluate. Enter a question mark
(?) to list names. Expression may include the wildcard
character (*) (e.g., to remove both c1 and c2, enter c*, but
the expression c1,c2 is not valid).
The new coordinates are computed and stored in the molecular
definition.
Show and VISUALIZE EXTENSION_POINT mol_area name ON|OFF
Hide:
Remove: REMOVE EXTENSION_POINT mol_area name

13.3.4 Define a Line

A line is defined by a dummy atom at a specified distance along the path
between two atoms.

Define DEFINE LINE origin_atom positive_atom dist name

comment
• origin_atom—Atom at the origin of the line.
• positive_atom—Atom defining the direction of the line
from origin_atom.
• dist—Distance (Å) from origin_atom to dummy atom.
Positive value indicates “towards” positive_atom, a
negative value corresponds to “away from.”
• name—The name to give to the line. Names must start with
an alphabetic character and may contain digits and under-
scores.
• comment—A descriptive string associated with the line
that may contain any characters and be of arbitrary length.
Enclose the string in double quotes when entering spaces or
special characters.
Re-Evaluate: EVALUATE LINE mol_area name
• mol_area—Area(s) containing line(s) to evaluate.
• name—Name of line(s) to evaluate. Enter a question mark
(?) to list names. Expression may include the wildcard
character (*) (e.g., to remove both c1 and c2, enter c*, but
the expression c1,c2 is not valid).
The new coordinates are computed and stored in the molecular
definition.
Show and VISUALIZE LINE mol_area name ON|OFF
Hide:
Remove: REMOVE LINE mol_area name

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 13. Geometry: Measure, Modify, Define Features
Geometric Features: Define and Modify

13.3.5 Define a Plane

A plane is represented by four dummy atoms connected by four dummy bonds
delineating a parallelogram. (See Tailor subject PLANE to alter the character-
istics of the plane.) The plane is stored as four dummy atoms, four dummy
bonds, and a feature in the molecular description. Dummy atoms have the type
Du and are colored magenta.

Define via the Edit > Plane > Define

Menubar:
Define via Com- DEFINE PLANE atom_expr name comment
mand: • atom_expr—The atoms to use in calculating the plane
equation: from a minimum of 3 non-linear atoms up to
all the atoms in the molecule.
• name—The name to give to the plane. Names must
start with an alphabetic character and may contain
digits and underscores.
• comment—A descriptive string associated with the
plane that may contain any characters and be of
arbitrary length. Enclose the string in double quotes
when entering spaces or special characters.
The four dummy atoms are named “name” followed by 1,
2, 3, or 4.
The equation of the least squares plane is printed in the
console along with the RMS distance of the defining
atoms to the plane.
Re-Evaluate: EVALUATE PLANE mol_area name
• mol_area—Area(s) containing plane(s) to evaluate.
• name—Name of plane(s) to evaluate. Enter a question
mark (?) to list names. Expression may include the
wildcard character (*) (e.g., to remove both c1 and c2,
enter c*, but the expression c1,c2 is not valid).
Use this feature to update the plane equation and dummy
atom coordinates after whole or partial re-orientation of
the molecule (via Fit Atoms, Freeze Molecule, ORIENT,
geometrical modification or manipulation of rotatable
bonds). Lines normal to a plane, if present, must be re-
evaluated via the EVALUATE NORMAL command.
Show and Hide: VISUALIZE PLANE mol_area name ON|OFF
Remove via the Edit > Plane > Delete
Menubar:

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13. Geometry: Measure, Modify, Define Features
Geometric Features: Define and Modify

Remove via REMOVE PLANE mol_area name

Command: Any features (e.g., constraints) attached to that plane are
deleted along with the plane. If an atom, real or artificial,
and involved in a plane definition, is removed, the plane is
removed automatically.

Additional Information:
• Define the Normal to a Plane on page 164 for using a plane to define a
normal
• Reflect Atoms Through a Plane on page 126

13.3.6 Define the Normal to a Plane

A normal is a line normal to an existing plane through an atom.The normal is
represented by two dummy atoms on either side of a specified atom. Two
dummy bonds connect them to the midpoint. The bonds are perpendicular to the
specified plane. Distance from the midpoint to the dummy atoms is a variable
set at 1 Å by default. The normal is stored as two dummy atoms, two dummy
bonds and a feature in the molecular description. Dummy atoms have the type
Du and are colored magenta.

Define via the Edit > Normal > Define

Menubar:
Define via Com- DEFINE NORMAL atom_sel plane_name
mand: normal_name comment
The two dummy atoms are named “normal_name” fol-
lowed by 1 or 2.
• plane_name—The name of an existing plane. Enter a
question mark (?) to obtain a list.
• normal_name—The name to give to the normal.
Names must start with an alphabetic character and may
contain digits and underscores.
• comment—A descriptive string associated with the
normal that may contain any characters and be of
arbitrary length. Enclose the string in double quotes
when entering spaces or special characters.

164 SYBYL Basics SYBYL-X 2.1

 13. Geometry: Measure, Modify, Define Features
Geometric Features: Define and Modify

Re-Evaluate: EVALUATE NORMAL mol_area name

• mol_area—Area(s) containing normal(s) to evaluate.
• name—Name of normal(s) to evaluate. Enter a
question mark (?) to list names. Expression may
include the wildcard character (*) (e.g., to remove both
c1 and c2, enter c*, but the expression c1,c2 is not
valid).
Plane coordinates and plane normal lines are not updated
after whole or partial re-orientation of the molecule (via
Fit Atoms, Freeze Molecule, ORIENT, geometrical modifi-
cation or manipulation of rotatable bonds). Use the EVAL-
UATE PLANE command first then re-evaluate the normal
line(s).
Show and Hide: VISUALIZE NORMAL mol_area name ON|OFF
Remove via the Edit > Normal > Delete
Menubar:
Remove via REMOVE NORMAL mol_area name
Command: Any features (e.g., constraints) attached to that normal are
removed as well. If an atom, real or artificial, and involved
in a normal definition, is removed, the normal is removed
automatically.

Additional Information:
• See Define a Plane on page 163 for information about how to define the
required plane
• See Tailor subject NORMAL to alter the characteristics of the normal

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13. Geometry: Measure, Modify, Define Features
Geometric Features: Define and Modify

13.3.7 UNITY Query Features

A UNITY geometrical feature or constraint for a structure is used within a
UNITY database query. UNITY features are displayed as background objects
and can be saved as part of the molecular definition. Tailor subject UNITY can
be used to select the color for highlighting constraints, features, and receptor
sites.

Define UNITY Query Features

For details on defining specific features and constraints, see the “UNITY
Queries” chapter in the UNITY Manual.

Menubar: UNITY > Edit Query > Add Features

Command: DEFINE UNITY_FEATURE option

Features:

4_POINT_ANGLE_CON EXCLUDED_VOLUME_C RECEPTOR_SITE

STRAINT ONSTRAINT

ACCEPTOR_ATOM EXTENSION_POINT SPATIAL_CAP

ACCEPTOR_SITE FRAGMENT SPATIAL_LINE

ANGLE_CONSTRAINT HYDROPHOBIC SPATIAL_PLANE

AROMATIC LINE SPATIAL_POINT

BOND_PATH LP_ANGLE_CONSTRAI STERIC_FEATURE

NT

CENTROID NEGATIVE_CENTER SURFACE_VOLUME

CONTAINING_VOLUME NORMAL_POINT TETRAHEDRAL

_CONSTRAINT

DISTANCE_CONSTRAI PARTIAL_MATCH_CON TORUS

NT STRAINT

DONOR_ATOM PLANE

DONOR_SITE POSITIVE_N

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 13. Geometry: Measure, Modify, Define Features
Geometric Features: Define and Modify

Delete Non-Query Atoms

Menubar: UNITY > Edit Query > Delete > Atoms not in the
Query
The list of atoms to remove is displayed in the atom
expression dialog and highlighted on the molecule.
Changes to the atom expression may be made before
pressing OK to remove the atoms.
Command: REMOVE NON_QUERY_ATOMS mol_area
• mol_area—Area containing the UNITY query.
A list of atoms to remove is displayed in the atom expres-
sion dialog and highlighted in the molecule. Changes to
the atom expression may be made before pressing OK to
remove the atoms. If the molecule area does not contain
any UNITY features or constraints, no action is taken.

Modify UNITY Query Features

Menubar: UNITY > Edit Query > Manage Features

Command: MODIFY UNITY_FEATURE mol_area feature/con-
straint [{attribute value}] [color]
• mol_area—Molecule area containing feature or
constraint.
• feature/constraint—Feature or constraint to modify.
• attribute—Name of an attribute. Modifiable attributes
are type-specific, and depend on feature or constraint
selected.
• value—Value for the attribute.
• color—Optional for UNITY features only.

Delete UNITY Query Features

Menubar: UNITY > Edit Query > Delete > Features

UNITY > Edit Query > Manage Features
Command: REMOVE UNITY_FEATURE mol_area name
• mol_area—Area containing feature or constraint.
• name—Name of UNITY feature or constraint to
delete. Type ALL instead of a single name to delete all
features and constraints.
Any constraints based on that feature are removed as well.
If an atom, real or artificial, and involved in a feature or
constraint definition, is removed, the feature or constraint
is removed automatically.

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 14. Get Information on SYBYL Objects
• Definitions of SYBYL Objects on page 170
• Information on individual Objects on page 174
• Right-Click for Information on page 174
• Atoms, Bonds, or Substructures on page 174
• List Information About SYBYL Objects on page 175
• Print Information About Objects to a File on page 176

SYBYL-X 2.1 SYBYL Basics 169

14. Get Information on SYBYL Objects
Definitions of SYBYL Objects

14.1 Definitions of SYBYL Objects

Molecule Areas
Work spaces which hold structures being manipulated. Areas are designated by
the letter M followed by an integer. Any number of molecule areas can be
defined at any time, since SYBYL can handle an unlimited number of
molecules simultaneously. They may be assigned in arbitrary order, and will
hold any named entity supplied either from an external file, through
construction internally, or from a database. A molecule area may contain a
single atom, multiple fragments, water molecules, ions, or other components,
and structures with unfilled valences.

Atoms
The fundamental building blocks of molecules. You may name them arbitrarily
and specify their type. The SYBYL atoms types are defined in the file
$TA_DEMO/metals.tpd. Atoms can exist as bonded entities or singly.

Bonds
Connection between atoms to form molecules. Bond types (single, double,
triple, amide, aromatic, dummy, or non-chemical) are determined by the types
of atoms they join. Bond types determined automatically by the program can be
overridden to accommodate exceptional circumstances in a particular molecule.

Substructures
Group of atoms in which it is possible to reach any atom from any other atom
along a bonded pathway. No atom in a molecule can belong to more than one
substructure. A substructure may be a single atom, molecule fragments,
functional groups, a residue in a biopolymer, or the ligand in a protein-ligand
complex. Substructures are included in the molecular description to help
subdivide problems into manageable sizes and easily reference pieces of the
molecule.

Substructures are created and managed by SYBYL without intervention. For

example, when constructing a biopolymer from residues defined in a dictionary
or reading one in from a standard biopolymer structural file such as the RCSB,
each residue is a substructure. An example of the substructure assignment for a
short peptide sequence is shown below (substructure boundaries marked by
parentheses).

170 SYBYL Basics SYBYL-X 2.1

 14. Get Information on SYBYL Objects
Definitions of SYBYL Objects

In the case of non-polymers, the only control you have over the creation and
designation of substructures is in the order you construct the molecules or in
fragments chosen from the standard fragment library. All fragments in the
fragment library are designated as substructures. There is no unique assignment
of substructures to molecules. One person might assign them differently from
another. For example, the figure below shows two copies of a single molecule
which have been partitioned differently into substructures. Neither one is neces-
sarily a better choice than the other; they are merely different.

Features
Features are molecular characteristics. They can be based on atoms, other
features, or contain other information.
• Center of mass, centroid, extension point, line, normal, plane, and
various UNITY features
• Force field angle, distance, range, periodic boundary conditions and
torsional constraints
• Sets, including aggregates
• Search anchor atom, rotatable bonds, ring closure and distance
constraints
• Crysin unit cell parameters and space group
• Associated data file locations

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14. Get Information on SYBYL Objects
Definitions of SYBYL Objects

• Associated dictionaries
• Alternate atom types

Rings
SYBYL detects the formation and records the presence of rings at all times in
all molecules. Rings have wide-ranging implications for conformational manip-
ulations as well as modification of internal parameters, such as bond lengths and
angles, and they play an important role in identifying similarities among
molecules.
• Internal ring—A ring completely contained within a substructure.
Atoms and bonds in an internal ring are distinguished by the character *
next to their name in the atom or bond list.
• External ring—A ring which spans substructure boundaries. Typically
occur in polymers which are cross-linked (e.g., a peptide structure which
has one or more disulfide bridges). Atoms and bonds in an external ring
are distinguished by the character @.

The figure below illustrates both internal and external rings. The boxes
delineate substructure (monomer) boundaries in this peptide fragment. The
phenyl group in the phenylalanine monomer is an internal ring since it occurs
completely within the confines of a substructure. The heavy, dark bonds
indicate a ring formed by the cross-linking of the peptide by a disulfide bridge
between two cysteine monomers. It is termed an external ring because it crosses
substructure boundaries.

Sets
Named collections of objects substructures, atoms or bonds used for identifying
and naming important groups in a molecule. A set can be used as a shorthand
notation for groups of atoms, bonds, or substructures which are referenced
often.
• Static sets—Membership is identified at the time of definition. Once
specified, this membership does not change unless one of the elements
(atoms, bonds, substructures) is deleted from the molecule. For example,

172 SYBYL Basics SYBYL-X 2.1

 14. Get Information on SYBYL Objects
Definitions of SYBYL Objects

identify the amino acids in the active site of an enzyme and name them
for quick access.
• Dynamic sets—Membership is defined in terms of a rule and evaluated
at the time of reference. For example, the environment around a
particular atom in a molecule can be defined as a set using a sphere of
specified radius. As the molecule’s conformation is manipulated, the
membership in the set may change. When you reference this set’s name,
the contents of the volume are identified by evaluating the rule at that
time. The built-in sets in SYBYL are dynamic sets: Aromatic, H-bonds,
Backbone, Sidechain, Rings, Bumps, and Metals.

See Sets in SYBYL on page 207 for more details.

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14. Get Information on SYBYL Objects
Information on individual Objects

14.2 Information on individual Objects

See also the List Information About SYBYL Objects on page 175.

14.2.1 Right-Click for Information

No selection is required. The information pertains only to the clicked-on atom.

Atom right-click > Molecule Properties

A dialog displays the name of the molecule and the computed values of
several physical and chemical properties.

Atom right-click > Substructure Properties

A dialog displays the name of the substructure the clicked-on atom belongs
to and the ID number of the substructure’s root atom. If the molecule
containing the clicked-on atom is a biopolymer the information includes the
residue type and ID number as well as the chain name.

Atom right-click > Atom Properties

A dialog displays the atom’s name and that of the molecule it belongs to as
well as several computed properties.

14.2.2 Atoms, Bonds, or Substructures

Report information about the specified object in the console.

Menubar: Options > Info

• Atom then click the atom(s) of interest
• Bond then click two bonded atoms
• Substructure then click any atom in the substructure
(residue) of interest.
Press End to terminate the information loop.
Command: INFORMATION object_type object_sel
• object_type—ATOMS, BONDS, SUBSTRUCTURES.
• object_sel—ID for individual object. Prompting continues
until you enter the end-loop character (|).

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 14. Get Information on SYBYL Objects
List Information About SYBYL Objects

14.3 List Information About SYBYL Objects

List the requested information in the command console.

Menubar: Options > List

Command: LIST object_type object_expr [mode]
• object_type—AGGREGATES, ATOMS, BACKGROUNDS,
BONDS, BUILT_IN_SETS, CENTER_OF_MASS, CENTROID,
CONSTRAINT, EXTENSION_POINT, GLOBAL_SETS, LINE,
LOCAL_SETS, MOLECULES, NORMAL, PLANE, SEQUENCE,
SUBSTRUCTURES, TABLE, TAILOR, UNITY_FEATURE,
VIOLATIONS.
• object_expr—Particular set of objects of object_type to
list.
• mode—BRIEF (one line summary for each object or FULL
(all available information for each object) for most
objects. ALL, TYPE, or NAME for UNITY features. (In
picking mode, NAME allows picking on the screen of a
particular feature.)
The PRINT command is redundant with the LIST command.

In the atom, bond, and substructure list, an asterisk (*) in the column following
the ID indicates that the object belongs to an internal ring (i.e., a ring totally
contained within a substructure), whereas an “at” sign (@) indicates an external
ring (i.e., a ring which spans substructure boundaries). Substructures cannot
participate in internal rings but they can be members of external rings.

For sets, an asterisk (*) in the column after the ID indicates that the set is
defined and managed by the system.

Additional Information:
• Information on individual Objects on page 174
• Record the Output from a Single Command on page 204 to copy the
listing into a file
• Geometric Features: Define and Modify on page 159
• Tailor variable GENERAL ATOM_IDENTIFIER to alter the characteristics
of atom listings

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14. Get Information on SYBYL Objects
Print Information About Objects to a File

14.4 Print Information About Objects to a File

List the requested information in the command console and write it to the file
SYBYLPRINT.LIS in the current directory. Subsequence invocations of this
command will overwrite the file’s content.

PRINT object_type object_expr [mode]

object_type Type of object to include in the output:

AGGREGATES, ATOMS, BACKGROUNDS, BONDS,
BUILT_IN_SETS, CENTER_OF_MASS, CENTROID, CON-
STRAINT, EXTENSION_POINT, GLOBAL_SETS, LINE,
LOCAL_SETS, MOLECULES, NORMAL, PLANE, SEQUENCE, SUB-
STRUCTURES, TABLE, TAILOR, VIOLATIONS.
object_expr Objects to include in the output.
mode Listing mode to use (BRIEF or FULL). This argument does not
apply to all objects.

Use the full generality of the object expression syntax to determine which
objects to include.

In the atom, bond, and substructure list, an asterisk (*) in the column following
the ID indicates that the object belongs to an internal ring (that is, a ring totally
contained within a substructure), whereas an “at” sign (@) indicates an external
ring (a ring which spans substructure boundaries). Substructures cannot partic-
ipate in internal rings but they can be members of external rings.

For sets, an asterisk (*) in the column after the ID indicates that the set is
defined and managed by the system.

Additional Information:
• Information on individual Objects on page 174
• Tailor variable GENERAL ATOM_IDENTIFIER to alter the characteristics
of the listings

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 15. Use Molecule Databases
• Database Formats on page 178
• Open and Close SYBYL Databases on page 179
• Retrieve Molecules from a SYBYL Database on page 182
• Obtain Information on Databases on page 186
• Manage Database Content on page 187
• Save Database Molecules to Mol2 Files on page 191
• The DATABASE Command on page 193
• Database Qualifiers on page 192
• System Utilities on page 194

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15. Use Molecule Databases
Database Formats

15.1 Database Formats

There are currently two different formats for molecule databases:
• mol2dbms—A directory of Mol2 files, containing individual molecules,
and several other utility text files. Often referred to as a Mol2 database.
The directory name identifies the database. This format was introduced
in SYBYL 6.1.
• mdbms—A single file, binary format, introduced in SYBYL 5.x.

Note: To explore chemical and biological databases use UNITY, the search and
analysis system. See the UNITY Manual.

Because Mol2 databases are composed of text files, they are more portable
across different machine platforms than binary databases (e.g., Mol2 databases
are portable across platforms, whereas binary databases are not).

Mol2 databases are less susceptible to corruption than binary databases and are
more recoverable in case of corruption, since molecules can be held in separate
files. However, manipulating files within a Mol2 database via the system shell
while the database is open can generate error messages. Closing the database
(and any spreadsheet or table file (.tbl) using the database) and reopening it
usually eliminates such errors.

You can create a Mol2 database using the DATABASE CREATE and DATABASE
XCREATE commands, or from the system shell using existing Mol2 files created
by other parts of SYBYL. Also see Tailor subject DATABASE for information
about the MULTIMOL2 variable and how it affects Mol2 databases created from
the system shell.

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 15. Use Molecule Databases
Open and Close SYBYL Databases

15.2 Open and Close SYBYL Databases

15.2.1 Open a SYBYL Database
Notes about Databases:
• The database that is opened becomes the default user database.
• If the database is already open, the access mode of the open database is
changed to the newly specified mode.
• Any number of users may have the same database open READONLY.
However, if one user has a database open in APPEND or UPDATE
mode, nobody else has any access to it until the database is closed. If
one user has a database open in READONLY mode, nobody else is
allowed to open it in APPEND or UPDATE mode.
• SYBYL attempts to assign an alias to the newly opened database using
the base name of the full database name. For example, if the full
database name is /usr/me/mydb.mdb, SYBYL attempts to assign it
the alias “mydb”. This makes using database qualifiers easier. See the
ALIAS subcommand for more information about database aliases.

Additional Information:
• Tailor subject DATABASE to alter characteristics of the database opening
• To unlock a database that was not properly closed because of a system
crash, enter the following in a console: $TA_BIN/dbunlock
• DATABASE OPEN assigns a value to the UIMS2 variable
DATABASE_NAME

Via the Menubar

File > Database > Open

The Database Selection dialog that is displayed is very similar to the dialog for
opening files (see the Open File dialog description).

Via the Command Line

User Database: DATABASE OPEN filename access_mode

• filename—Database to open (default extension is
.mdb).
• access_mode—How database is accessed: READONLY,
APPEND, or UPDATE.

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15. Use Molecule Databases
Open and Close SYBYL Databases

System Data- DATABASE SYSTEM system_db access_mode

base: • system_db—Tripos-supplied database that becomes a
“user” database: FRAGMENT_LIBRARY or
GROUP_LIBRARY. (When opened, it becomes the default
database.)
• access_mode—How database is accessed: READONLY,
APPEND, or UPDATE.
Using APPEND or UPDATE prevents others from accessing
the system database, either directly or through FRAGMENT or
ADD GROUP commands, until database is closed.
Note: Care should be exercised when modifying the Tripos-
supplied databases, since much of the program’s operation
depends on their contents.

Create a New, Empty Database

Menubar: File > Database > New

Command: DATABASE CREATE filename
filename—Name for database file. Default extension .mdb
is provided automatically.
or: DATABASE XCREATE dbtype filename
• dbtype—Database format: MDBMS or MOL2DBMS.
• filename—Name for database file. Default extension
.mdb is provided automatically.

The database that is created becomes the default user database. It is automati-
cally opened in UPDATE mode; there is no need to open the database after
creation. If a file already exists with the given file name, you have a choice of
replacing the old one or issuing the command again to give another file name.
Replacing the old file creates a new file with that same name and deletes the
contents of the old file.

UIMS2 variable:
• The DATABASE CREATE and DATABASE XCREATE commands assign a
value to the UIMS2 variable DATABASE_NAME.

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 15. Use Molecule Databases
Open and Close SYBYL Databases

15.2.2 Copy Database Contents to a New Database

DATABASE TO_MOL2DB source destination

source File specification for the source database.

destination File specification for new database, i.e., the Mol2 database.
If file exists, you can replace the old one or issue the com-
mand again to give another file name. Replacing old file
creates a new file with that same name and contents of old
file are deleted.

15.2.3 Define a Database Alias

DATABASE ALIAS db_name alias

db_name Name or alias of an open user database.

alias New alias.

Aliases are useful in conjunction with database qualifiers. An alias can be used
in a qualifier instead of the full database name. A database can only have one
alias. If the specified database already has an alias, the old alias is overwritten.
A user assigned alias is lost when a user database is closed.

15.2.4 Specify the Default Database

Menubar: File > Database > Default

Command: DATABASE DEFAULT db_name

Database operations are applied to the default database if no database is

explicitly specified in a command.

UIMS2 Variable:
• DATABASE_NAME.

15.2.5 Close a SYBYL Database

Menubar: File > Database > Close

Command: DATABASE CLOSE
or: DATABASE XCLOSE db_name

If the default database is closed and other databases are open, one is arbitrarily
selected as the new default user database.

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15. Use Molecule Databases
Retrieve Molecules from a SYBYL Database

15.3 Retrieve Molecules from a SYBYL Database

15.3.1 Retrieve a Molecule

Menubar: File > Database > Get Molecule

Command: DATABASE GET expression [{selection_query}]
[mol_area]
• expression—Database query expression specifying
molecule(s) to retrieve (may include database qualifier,
otherwise default database is assumed).
• selection_query—
ASSIGN—Use SELECT and UNSELECT to specify
molecules to assign.
QUIT—Exit DATABASE GET without loading any
molecules.
RETRIEVE—Retrieve multiple molecules from open
database. To retrieve all molecules in a selection, enter
molecule area for first molecule. Other molecules are
placed in alphabetical order in consecutive work areas.
Previous contents of molecule areas are overwritten.
SELECT—Choose subset of currently selected
molecules. Selection can be a multi-step process.
UNSELECT—Return to set of molecules obtained by last
SELECT command. Can be used as many times as
SELECT.
• mol_area—Molecule area where first (or single)
retrieved molecule is placed (skipped if no molecule
present).

This command behaves differently depending on whether the expression maps

to a single molecule, no molecule, or multiple molecules.
• Single molecule, you are prompted for the molecule area to hold the
molecule.
• No molecules, a message indicates that molecule could not be found.
• Multiple molecules are listed on the terminal and you have access to
additional commands to narrow the selection. Retrieved molecules are
placed in consecutive molecule areas, starting with the one specified
when you entered the command.

Additional Information:
Database Query Expressions on page 183

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 15. Use Molecule Databases
Retrieve Molecules from a SYBYL Database

15.3.2 Search for Molecule(s) to Retrieve

DATABASE SEARCH search_mode name_expr [action]

search_mode How to search the database:

• NAME—Search by molecule name.
• MENU—Search using menus. The menus provide a
hierarchical structure within databases. The FRAGMENT
command, for example, uses a menu structure to
control searching of the fragment database. Menus are
formed by evaluating molecule groups (sets and
classes). A class which is the union of several groups
appears on a menu listing the component groups. A
group consisting of molecules appears as a menu of
molecule names. Selections continue recursively until
the final molecule is chosen.
name_expr Initial query of the molecule/group name (may include
database qualifier, otherwise default database is assumed).
action Varies depending on the search_mode.

This command is useful for browsing through an unfamiliar database, as well as

for setting up groups which are otherwise difficult to define.

15.3.3 Database Query Expressions

Database query expressions retrieve information about molecules in a database.
The molecules can be retrieved, placed into a group, or simply examined by
name. Molecules can be identified by whole or partial names, by membership in
defined groups, or by a combination of these.

The simplest form of a query expression is a molecule name, which specifies a

single molecule. When specifying a name to retrieve a molecule from the
database, names containing blanks and special characters, such as hyphens or
parentheses must be enclosed in double quotes. Names beginning with letters
and followed by nothing but letters, digits, or underscores may be used without
quotes. This is necessary to distinguish characters in names from operators in
database query expressions.

The next level of complexity in query expressions allows wildcards in molecule

names (but not group names). Finally, operations on groups provide a powerful
technique to designate molecules. They can consist of the logical operators
union, intersection, difference, and negation and the elements to which they are
applied.

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15. Use Molecule Databases
Retrieve Molecules from a SYBYL Database

The Venn diagrams below illustrate the logical operators. A, B, and C are
general object sets. Shaded areas represent the selected set D which results from
the indicated operations. The outer circle represents the total set from which the
subsets are chosen.

Union Intersection Difference Negation

In either set In both sets In first set and Do not have speci-
not in second fied property
D=A+B or D=A&B D=A-B D=~A
D=A,B

In database query expressions, operators are evaluated from left to right, with
operations of highest precedence evaluated first. The order of operator prece-
dence is (from highest to lowest):

Negation ~ highest
Intersection &
Union, Difference +– lowest

Parentheses group the elements of the expression for evaluation in a specified

order.

Examples
Retrieve tryptophan from current database and place it in M1.
DATABASE GET (tryptophan) m1

Retrieve all molecules whose names begin with t (or T) from current database.
For multiple matches, you are asked to select one.
DATABASE GET (t*) m1

Retrieve all molecules whose names begin with h (or H) and are members of the
group substrate from current database. For multiple matches, you are asked to
select one molecules.
DATABASE GET (substrate & h*) m1

Retrieve all molecules whose names begin with 1,4,5 T and are members of the
group reaction1 or reaction2 (or both). Use parentheses to ensure the union
operation takes place before the intersection.

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 15. Use Molecule Databases
Retrieve Molecules from a SYBYL Database

DATABASE GET (“1,4,5 T*” & (reaction1 + reaction2))

Double quotes around the (partial) molecule name are required since it contains
special characters.

15.3.4 Load the Database into a Spreadsheet

Each row in the spreadsheet corresponds to a Mol2 file in the database.
Properties may then be computed and stored in columns.

Menubar: File > Import File

Set File of Type to Database and select a .mdb direc-
tory.
Command: DATABASE TABLE

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15. Use Molecule Databases
Obtain Information on Databases

15.4 Obtain Information on Databases

15.4.1 List All Open Databases
DATABASE ALLOPEN

Full database names are listed along with aliases given in parentheses. The
default user database is denoted.

15.4.2 List Contents of an Open Database

Menubar: File > Database > List

Command: DATABASE DIRECTORY item_type name_expr
• item_type—ANY, CLASS, MOLECULE, SET.
• name_expr—Expression of names of items to list (may
include database qualifier, otherwise default database is
assumed).

15.4.3 List Molecule and Group Information for an Open Database

DATABASE SHOW item_type name_expr [listing_mode]

item_type ANY, CLASS, MOLECULE, SET.

name_expr Expression specifying names of items to list (may include
database qualifier, otherwise default database is assumed).
listing_mode • BRIEF—Abridged information about selected items,
one-item-per-line.
• FULL—Detailed listing for each item (for ANY or
MOLECULE only).

15.4.4 List Information About an Open Database

Default Database: DATABASE STATUS

Any Open Database: DATABASE XSTATUS db_name
Lists contents, including the database filename, alias, format, access mode and
the number of molecules, sets, and classes currently defined.

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 15. Use Molecule Databases
Manage Database Content

15.5 Manage Database Content

15.5.1 Add Molecule(s) to a Database
Notes:
• The molecule being added must have a name. (See Name or Rename a
Molecule on page 124.)
• The database must be open in UPDATE mode, or APPEND mode is
sufficient if the molecule does not already exist in the database

Menubar: File > Database > Put Molecule

Add to Default DATABASE ADD mol_expr [disposition]
Database via Com- • mol_expr—Expression defining molecules to add to
mand: default user database (either a single molecule area
or a comma-separated list of areas).
• disposition—KEEP or REPLACE original molecule.
Add to Database DATABASE XADD db_name mol_expr [disposi-
via Command: tion]
• db_name—Name or alias of open user database.
• mol_expr—Expression defining molecules to add
(either a single molecule area or a comma-separated
list of areas).
• disposition—KEEP or REPLACE original molecule.
Name Molecule DATABASE SAVE_AS mol_area new_name [dispo-
and Add to Data- sition]
base via Com- • mol_area—Molecule area containing molecule to
mand: save.
• new_name—Name for molecule (may include
database qualifier, otherwise default user database is
assumed).
• disposition—KEEP or REPLACE original molecule.

Additional Information:
Mol2 Files on page 42

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15. Use Molecule Databases
Manage Database Content

15.5.2 Delete Molecule(s) in a Database

Menubar: File > Database > Delete Molecule

Command: DATABASE DELETE item_type name_expr NO | YES
• item_type—CLASS, MOLECULE, SET.
• name_expr—Expression of names of items to delete
(may include database qualifier, otherwise default user
database is assumed).

Deletion of groups from a database has no effect on the molecules which were
inside those groups. Molecules themselves must be explicitly deleted.

The database must be open in UPDATE mode for this command to operate
successfully.

15.5.3 Organize Molecules into Groups (Sets and Classes)

Additional Information:
Fragment Library on page 224

Grouping Mechanisms in a Database

Molecules in a database can be organized into groups by the user, providing a

convenient method for representing relationships between molecules. It is
important to recognize the distinction between the sets described below and the
sets of atoms, bonds, or substructures. Here the term “set” is used to refer to a
collection of molecules, not to a particular molecule’s constituents.
Database Sets—A named, static collection of molecules explicitly created
by the user. Examples might be groups called “current_project,”
“substrates,” or “minimized.” Members of a set may be specified by a
database query expression which is evaluated at that time to determine the
members of the set. To update the contents of a set, simply give it a new
definition which incorporates its own value. For example, the following
removes hydroxyproline from the set HYDROPHOBIC.
DATABASE DEFINE SET hydrophobic (hydrophobic-hydrox-
yproline)
Database Classes—Molecules matching a specified database query
expression. Once defined, the class is reevaluated each time it is referenced,
to reflect the current database contents.

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 15. Use Molecule Databases
Manage Database Content

Define/Modify Definitions of Groups in a Database

DATABASE DEFINE CLASS | SET name expr comment

name Name of the class or set.

expr Database query expression (may include database qualifier, other-
wise default database is assumed).
comment Short descriptive string explaining significance of class/set.

Note:
• Database must be open in UPDATE mode for this command to operate
successfully, or APPEND mode is sufficient if the molecule group does
not already exist in the database.
• Each time a defined class’ name appears in a database query expression,
it is reevaluated and its members determined for the database.
• If a molecule, defined as a member of a set, is deleted, that molecule is
automatically removed from the set.

Rename a Group or Molecule in a Database

Menubar: File > Database > Rename Molecule

Command: DATABASE RENAME item old_name new_name
• item—CLASS, MOLECULE, SET.
• old_name—Current name of group or molecule.
• new_name—New name for group or molecule.

Notes:
• If new_name for a molecule already exists in the database, you are asked
whether or not the new molecule should replace the current one.
• If new_name for a group already exists in the database, the operation
fails.
• Database must be open in UPDATE mode for this command to operate
successfully.
• Both names may contain a database qualifier. However, the operation
fails if the qualifiers do not refer to the same database.

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15. Use Molecule Databases
Manage Database Content

Reorganize and Compress Database Contents

DATABASE REORGANIZE filename

filename Name of the database file (default extension is .mdb).

Reorganizing and compressing the contents of a molecule database allows

unused space to be reclaimed.

mol2dbms:
• Mol2 files containing more than one molecule are broken into multiple
Mol2 files, one molecule per Mol2 file. This “flattens” the database.
• Mol2 files are renamed so file name matches (or nearly matches) name
of molecule in file.
• Reorganization can decrease access time, but has little effect on database
size, since Mol2 databases rarely accrue unused space.
• Reorganizing a Mol2 database is useful only when the database was
created by the user directly from the system shell. This is because Mol2
databases, created and accessed only via the DATABASE command, have
neither MultiMol2 files nor misnamed Mol2 files.
• Whenever SYBYL writes Mol2 files via the DATABASE command(s),
they are written with at least 6 digits of precision. If the value of the
tailor variable MOL COORD_PLACES is less than 6 (such as the default of
4), it is set to 6 during the operation of the DATABASE command and
reset when complete. If, however, the values higher than 6, the tailor’s
value is used throughout.
• Warning: The DATABASE REORGANIZE command creates a new Mol2
database with a temporary name. This name is generated in the directory
set by the environment variable TMPDIR. If the variable is not set, the
new database is created in the working directory. If this variable is
defined in your environment, that is where the new database ends up,
and hence appears to be lost.

mdbms:
• A consistency check ensures the database contents match the index
structure. This is the only accepted method of recovery for a corrupted
database (as indicated by the error message RECORD_KEY_ERROR).
• Database must not be open by any user when the REORGANIZE command
is given. The reorganized database overwrites the old file.
• Highly active databases should be periodically reorganized to recover
unused space. Compressing the files can have a significant impact on
access time.

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 15. Use Molecule Databases
Save Database Molecules to Mol2 Files

15.6 Save Database Molecules to Mol2 Files

Menubar: File > Database > Write MOL2 File
Command: DATABASE WRITE_FILE2 expression selection_query
[filename]
• expression—Molecule(s) to write out to file(s) (may
include database qualifier, otherwise default database is
assumed). Multiple molecules are listed in console.
• selection_query:
SELECT expr—Available if multiple molecules are
specified. Choose a subset of molecules. Expression
provided here is limited to currently specified molecules,
even though other database molecules might match.
Selection continues until either OUTPUT or QUIT is chosen.
UNSELECT—Available if multiple molecules are specified.
Return to set of molecules obtained by last SELECT
command. UNSELECT can be entered as many times as
SELECT was used to narrow the selection.
OUTPUT—Write selected set of molecules to file.
QUIT—Exit command without writing the file.
• filename—File to hold molecules (default extension is
.mol2). This argument is skipped if QUIT is entered.

Note: Mol2 files written via database operations have at least 6 digits of
precision. If the tailor variable MOL COORD_PLACES is set to < 6 (such as the
default of 4), it is set to 6 during the operation of the DATABASE command and
reset when complete. If the value is > 6, the tailor’s value is used throughout.

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15. Use Molecule Databases
Database Qualifiers

15.7 Database Qualifiers

A database qualifier is added to a query expression to explicitly specify the
database to which the expression applies. It consists of a database name (or
alias) placed before the query expression, separated from the query by the “!”
character. A query expression without a database qualifier automatically applies
to the default user database.

SYBYL first checks the names of open databases (which can be seen using the
ALLOPEN command). If the database qualifier matches a name of an open
database, that database is selected for the operation. If no open database name
matches, then the SYBYL checks the alias of any open database. If there is a
match, that database is selected for the operation. If no aliases of open databases
match, then the qualifier is considered to be invalid. (The same process applies
to the open database arguments of the ALIAS, DEFAULT, XADD, XCLOSE, and
XSTATUS subcommands.)

Note: Double quotes must be used when spaces occur in a database qualifier.
Also, if the special character “!” occurs in a molecule name, the molecule name
should be enclosed in double quotes.

Examples
Retrieve tryptophan from the default database and place it in M1. (No database
qualifier is needed.)
DATABASE GET (tryptophan) m1

Retrieve all molecules whose names begin with t (or T) from the database /usr/
me/mydb.mdb. For multiple matches, select one.
DATABASE GET /usr/me/mydb.mdb!(t*) m1

Retrieve the molecule named botulin from the database whose alias is toxins
and place it in M3. (A database such as /usr/me/project_xyz/toxins.mdb is
automatically assigned the alias toxins when opened.)
DATABASE GET toxins!botulin m3

See the OPEN and ALIAS subcommands for additional information about
database aliases.

192 SYBYL Basics SYBYL-X 2.1

 15. Use Molecule Databases
The DATABASE Command

15.8 The DATABASE Command

The DATABASE command provides functionality to manipulate molecule
databases, whether they have been supplied by Tripos or defined by the user.

DATABASE functions can be accessed in two ways:

• Precede each subcommand with the word DATABASE.
• Type MODE DATABASE to enter the DATABASE mode. To exit this mode,
type either the end-loop character (|) or ENDMODE. Selecting another
menu category also exits the DATABASE mode. When in DATABASE
mode, other SYBYL commands can be accessed by preceding them with
COMMAND.

Below is a list of the DATABASE subcommands:

ADD ENDMODE SYSTEM

ALIAS GET TABLE
ALLOPEN MATCH_ALIGN TO_MOL2DB
(QSAR Manual)
CLOSE OPEN WRITE_FILE
COMMAND RENAME WRITE_FILE2
CREATE REORGANIZE XADD
DEFAULT SAVE_AS XCLOSE
DEFINE SEARCH XCREATE
DELETE SHOW XSTATUS
DIRECTORY STATUS

SYBYL-X 2.1 SYBYL Basics 193

15. Use Molecule Databases
System Utilities

15.9 System Utilities

Since system commands like rm and cp behave differently when operating on
regular files versus directories (without additional flags), the following system
shell scripts are provided in $TA_BIN.
• db_rm removes molecular databases of either format:
db_rm db1 ... dbN
• db_cp copies a molecular database of either format:
db_cp source_db target_db

The format of target_db is the same as that of source_db. target_db is

overwritten if it already exists.

194 SYBYL Basics SYBYL-X 2.1

 16. Manage SYBYL Sessions
• Save a SYBYL Session on page 196
• What is Saved in a Session?
• What is Not Saved in a Session?
• Details About Saved Background Images
• Open (Restore) a Saved Session on page 200
• Delete a Saved Session on page 200
• Open a New Session on page 201
• Close a SYBYL Session on page 201
• Record and Play Back SYBYL Operations on page 202
• Record SYBYL Operations in a File
• Play Back a File of Recorded Operations
• Insert a Pause in a Recorded File
• Read Command Input From a Text File
• Record the Output from a Single Command
• Record the Console Dialogue of a Session

SYBYL-X 2.1 SYBYL Basics 195

16. Manage SYBYL Sessions
Save a SYBYL Session

16.1 Save a SYBYL Session

A SYBYL session, in its current state, can be saved in a specified directory.
This allows you to return to SYBYL at a later date and continue your work from
the point where you saved the session. See Open (Restore) a Saved Session on
page 200.

A log of saved sessions is stored in .sybyl/sessionHistory within your home

directory or folder. Different versions of this file are used by different versions
of SYBYL-X.

Save the Session

Menubar: File > Save Session

Or File > Save Session As
Toolbar Icon: or on the SYBYLtoolbar.
Command: SESSION SAVE dir_name

Each SYBYL session is saved in a directory. The default name for a session
directory is the current date and time (dd_mmm_yyyy_hh_mm). The extension
.ses is appended automatically. Saving a session changes the default directory
to that of the saved session.

The first Save Session ( )operation prompts for a directory name. Subse-
quent Save Session operations for the same session, whether newly created or
restored from a previously saved session, overwrite the same directory.

Use Save Session As ( ) to save the current session to a new directory.

Save the Session and Exit SYBYL

Command: SESSION SQUIT dir_name

Additional Information:
To specify a single default location (other than “current working directory”),
use the environment variable SAVE_SESSION_DIR, which must be set prior to
starting SYBYL.

196 SYBYL Basics SYBYL-X 2.1

 16. Manage SYBYL Sessions
Save a SYBYL Session

16.1.1 What is Saved in a Session?

A SYBYL session is a directory of files that contain the full specification
necessary to restore the session at a later time. For that purpose the following
are saved.
• All molecules in their displayed state are saved to individual .mol2 files
that include for all atoms their show/hidden status, color, labels, and
rendering mode.
• Data necessary to preserve rotatable bond angles and to restore dynamic
hydrogen bonds, distance and bump monitoring.
• Surfaces and ribbons associated with molecules as well as their show/
hidden status and color.
• Toolbars: position of all toolbars, visible status of all icons, user-defined
icons.
• Screen settings:
• Global and individual rotations and translations as well as scale
• Screen mode: full, quartered, etc.
• View mode: mono, orthographic, relaxed, and crossed stereo, (but
not stereo in a window) and associated settings
• Depth cue and Z-clipping
• Font, color and lighting
• Tailor variables and parameter files (.tpd)
• Spreadsheets
• The following types of background objects:
• Rulers
• MOLCAD surfaces
• Protein rendering
• Biopolymer ribbon
• Hbond
• Multiple volume surfaces
• Potential
• Dots
• QSAR contours

SYBYL-X 2.1 SYBYL Basics 197

16. Manage SYBYL Sessions
Save a SYBYL Session

16.1.2 What is Not Saved in a Session?

• Backgrounds images not supported:
• Generalized Surfaces
• Isosurfaces
• Surfaces representing CoMFA regions
• MOPAC
• AMPAC
• Force Field constraints
• Annotations

16.1.3 Details About Saved Background Images

MOLCAD Surfaces
• The surface style (lines, dots, etc.) and the current coloring property are
retained.
• If the color of a MOLCAD surface was changed with the BACKGROUND
COLOR command (not recommended), the color will not be restored
correctly.

Protein Rendering
• The following settings are taken from the time of creation:
• The opaque/transparency (TAILOR!RENDER!SURFACE_TYPE)
• Display of alpha helices (TAILOR!RENDER!HELIX_DISPLAY)
• Determination of secondary structure elements
(TAILOR!RENDER!SEC_STR_SRC)
• All other settings of TAILOR!RENDER are taken from the tailor.save
file at the time of the session saving:
• Coloring applied from data in a ProTable column is not retained.

Biopolymer Ribbon
• The number of strands and color are retained.
• Setting for TAILOR!RIBBON!RIBBON_WIDTH is taken from the
tailor.save file at the time of the session saving.

Hydrogen Bonds
• The atom set and color are retained.
• All settings of TAILOR!HBONDS are taken from the tailor.save file at
the time of the session saving.

198 SYBYL Basics SYBYL-X 2.1

 16. Manage SYBYL Sessions
Save a SYBYL Session

• The .dsp file is not saved, as the background will be recreated upon
restoration of the session.

QSAR Contours
• The graph field file must be saved during the contour creation. This file
is saved if the contour was created from the QSAR GRAPH FIELD
command. If the View CoMFA dialog was used, the Save to File(s)
check box must be on.
• The surface type used at creation is retained using the
TAILOR!CONTOUR!DISPLAY_AS setting.
• All TAILOR!TABLE and TAILOR!GRAPHS values are taken from the
tailor.save file at the time of the session saving.
• The .dsp and .cnt files are not saved, as the background will be
recreated upon restoration of the session.

Volume/Mvolume
• The volume color and surface type used at creation are retained using the
TAILOR!CONTOUR!DISPLAY_AS setting.
• Settings of TAILOR!VOLUME are taken from the tailor.save file at the
time of the session saving. However, volumes created with
TAILOR!VOLUME!MAP_RANGE set to FIXED_RANGE are not restorable.
• The .dsp and .cnt files are not saved, as the background will be
recreated upon restoration of the session.
• The filename originally used to create the .dsp/.cnt file is not retained.
A default name is used to guarantee that more than one of these surface
types can be restored without needing to prompt the user.

Potential
• The surface type used at creation is retained using the
TAILOR!CONTOUR!DISPLAY_AS setting.
• Settings of TAILOR!POTENTIAL are taken from the tailor.save file at
the time of the session saving.
• The .dsp and .cnt files are not saved, as the background will be
recreated upon restoration of the session.
• The filename originally used to create the .dsp/.cnt file is not retained.
A default name is used to guarantee that more than one of these surface
types can be restored without needing to prompt the user.
• These backgrounds are not restorable with TERM NO.

SYBYL-X 2.1 SYBYL Basics 199

16. Manage SYBYL Sessions
Open (Restore) a Saved Session

Dots
• The coloring method used at creation is retained.
• Settings of TAILOR!DOTS are taken from the tailor.save file at the time
of the session saving.
• The .dot file is not saved, as the background will be recreated upon
restoration of the session.
• The filename originally used to create the .dot file is not retained. A
default name is used to guarantee that more than one of these surface
types can be restored without needing to prompt the user.

16.2 Open (Restore) a Saved Session

Previously saved SYBYL sessions can be restored using either of the following.

Menubar: File > Open Session

The 5 most recent sessions are listed on the File menu
in reverse chronological order.
Toolbar Icon: on the SYBYL toolbar.
Command: SESSION RESTORE dir_name

Each saved SYBYL session is stored in a directory with the .ses extension. See
Save a SYBYL Session on page 196.

During restoration:
• The current working directory is changed to the location of the restored
session’s directory.
• Prompts are also presented regarding the deletion of any currently
displayed molecules, background images, and spreadsheets before
continuing.

16.3 Delete a Saved Session

To delete a saved session simply delete the session directory.

200 SYBYL Basics SYBYL-X 2.1

 16. Manage SYBYL Sessions
Open a New Session

16.4 Open a New Session

Open a new SYBYL window where you can perform work independently of the
current session.

Menubar: File > New > Session

Toolbar Icon: on the SYBYL toolbar.

If licensing does not allow for an additional SYBYL window a dialog will
inform you that the session limit has been reached.

See License Requirements for SYBYL Basics on page 9.

16.5 Close a SYBYL Session

If you have multiple SYBYL sessions open simultaneously you must close each
of them individually.

File > Close Session

Closing a session performs the following operations:

• Prompts whether to save the current session so that the current state of
SYBYL reloaded at a later time. See Manage SYBYL Sessions on page
195 for more details.
• Deletes all molecules and background objects (Edit > Delete Every-
thing).
• Closes all spreadsheets and associated databases.
• Reset the directory that the default when SYBYL was launched.

Closing a session does not exit SYBYL.

SYBYL-X 2.1 SYBYL Basics 201

16. Manage SYBYL Sessions
Record and Play Back SYBYL Operations

16.6 Record and Play Back SYBYL Operations

SYBYL includes scripts for tracking commands and playing back recorded
operations. These are useful for documenting a session and when tracking
potential problems in the use of SYBYL. It is important to activate these
options at the beginning of your SYBYL session.

A collect/take file consists of a series of command lines where each command

must appear on a single logical line. Lines are terminated by an end-loop
character (|) unless the last character on the line is a back slash (\).

The following characters, when first on one line, have special meaning in a
collect file:
# ignore the line, typically used for comments,
% if current session is interactive ask user for confirmation before
continuing, typically used to pause during playback.

Additional Information:
Automatic Command Execution at SYBYL Startup on page 26

16.6.1 Record SYBYL Operations in a File

When this option is enabled, all commands and arguments are captured into a
file which can be replayed to reproduce a session. The file closes automatically
at the end of the SYBYL session.

Menubar: Options > Record Macro

Command: COLLECT action [filename]
• action:
APPEND—Reopen existing file and continue journaling.
COMMAND—Force collection of next command even if
collection was suspended.
FILTER—ON/OFF; whether to collect all SPL
constructs.
FORCE_RESUME—Resume journaling even if multiple
SUSPEND commands were made.
ON—Enable journaling of command input in file.
OFF—Stop journaling of commands and close file.
RESUME—Cancel last SUSPEND.
SUSPEND—Temporarily suspend journaling without
closing file.
• filename—File to receive journaled commands. Default
extension is .col.

202 SYBYL Basics SYBYL-X 2.1

 16. Manage SYBYL Sessions
Record and Play Back SYBYL Operations

To store actions of menu picks in a collect file, first issue the command MENU
COLLECT ON.

Only one COLLECT file can be open at a given time.

UIMS2 Variable:
• UIMS2_COLLECT_FILE—Name of the current collect file.

Additional Information:
• Record the Console Dialogue of a Session on page 205
• Read Command Input From a Text File on page 204
• Insert a Pause in a Recorded File on page 204
• Play Back a File of Recorded Operations on page 203

16.6.2 Play Back a File of Recorded Operations

A recorded session can be used to repeat a series of commands on several
different molecules, to replay a demonstration script, or to recover one’s
position lost as a result of system failure.

Menubar: Options > Load Macro

Command: TAKE filename

When an incomplete command line is encountered in the file, interactive

prompting takes place to finish the command before proceeding to the next
command line.

Use the command UIMS GUI_MODE to direct the prompts for input when
executing SPL scripts:
• FULL — prompt for command arguments in successive dialogs (default).
• OBJECT_ONLY — use a dialog only if an object (atom, bond,
substructure, molecule) is requested.
• NONE — direct the input of command arguments to the Command
Console. Use this option in SPL scripts to suppress the posting of dialog.

Additional Information:
• Record SYBYL Operations in a File on page 202
• Read Command Input From a Text File on page 204
• Insert a Pause in a Recorded File on page 204
• Record the Console Dialogue of a Session on page 205

SYBYL-X 2.1 SYBYL Basics 203

16. Manage SYBYL Sessions
Record and Play Back SYBYL Operations

16.6.3 Insert a Pause in a Recorded File

PAUSE delta_time

delta_time Number of seconds to pause program execution.

By inserting this command into the recorded session file, you can halt program
execution for a specified number of seconds or indefinitely, if delta_time is set
to zero. In this way, you can give the user ample time to read the comments.
PAUSE is used in preparation of demonstration scripts. Note: These scripts
cannot be played back in menu mode.

As an alternative to PAUSE, inserting the WAIT command suspends execution

until either C (continue), G (go), or Q (quit) is entered. Enter either command at
the keyboard during the recording session or edit the file afterwards.

Additional Information:
• Record SYBYL Operations in a File on page 202 to prepare a script
• Play Back a File of Recorded Operations on page 203 to play back a
prepared script

16.6.4 Read Command Input From a Text File

TTY filename
Input is read from the specified file (file extension must be included) until an
end-of-file condition is encountered. The text in the file is executed as if it was
manually entered by the keyboard. This is convenient when generating
command procedures without the use of the COLLECT command.

Warning:
TTY does not understand command context as does the TAKE command. Thus
any mistakes in the TTY file are faithfully executed.

Additional Information:
• Record SYBYL Operations in a File on page 202
• Play Back a File of Recorded Operations on page 203

16.6.5 Record the Output from a Single Command

The text output from a single command can be sent to a file. This is useful for
storing lengthy output of commands such as minimizers, LIST, TOPOGRAPHY,
etc.

CAPTURE filename command

204 SYBYL Basics SYBYL-X 2.1

 16. Manage SYBYL Sessions
Record and Play Back SYBYL Operations

filename File to receive output generated by specified com-

mand. No default file extension.
command A single SYBYL command with all its arguments.

Additional Information:
• List Coordinates, Distances, or Angles on page 156
• List Information About SYBYL Objects on page 175
• Record the Console Dialogue of a Session on page 205

16.6.6 Record the Console Dialogue of a Session

When this option is enabled, the complete dialogue is recorded in a file.
Program prompts, user responses, commands, and program output are recorded
in this file. It can be used to document sessions with the program as an adjunct
to a laboratory notebook. The file closes automatically at the end of the SYBYL
session.

Menubar: Options > Log Session

Command: PHOTO status [filename]
• status:
ON—Record console dialogue to specified file. Infor-
mation is first stored in a buffer. By default, buffer is
automatically flushed to the file as soon as it is full.
OFF—Terminate recording.
FLUSH—Write all currently buffered PHOTO infor-
mation immediately to file. Future I/O flushing is not
affected by this command.
LINEBUFFER—Line buffer pending and all future
PHOTO I/O, data is flushed continuously to file. LINEB-
UFFER is off initially. If you turn PHOTO OFF then back
ON, you must explicitly turn on LINEBUFFER again.
• filename—File to receive the console dialogue. There is
no default extension.

UIMS2 Variable:
• UIMS2_PHOTO_FILE—Name of the current photo file.

Additional Information:
• Record the Output from a Single Command on page 204
• Record SYBYL Operations in a File on page 202
• Play Back a File of Recorded Operations on page 203

SYBYL-X 2.1 SYBYL Basics 205

This page intentionally blank.
 17. Sets in SYBYL

A Set is a named collection of objects: atoms, bonds, or substructures. Examples

in the context of a biopolymer are sidechain atoms, backbone bonds, co-crystal-
lized water molecules, active site. A set can be used as a shorthand notation for
groups of atoms, bonds, or substructures which are referenced often.

Some sets are closely associated with the particular molecules for which they
are defined (local sets), while others may be applied in a blanket fashion to any
molecule (global sets). Once applied to a particular molecule, the definitions of
all sets are stored in the molecular description along with the coordinates and all
other molecular data.

When you reference a set name in the context of an operation, the members of
the defined set are automatically identified as the object of the action. If the
request is for atoms or bonds, the specified substructures are expanded to their
respective atom or bond constituents automatically.

The diagram below shows sets used in SYBYL and their interrelationships.

• Global Sets on page 209—Set whose definition is applicable on a

system-wide basis, i.e., it may be applied to any molecule. of special
interest are the Global Sets in the Biopolymer Dictionary on page 210.
• Local Sets on page 212—Created for specification of objects in a
particular molecule. Membership is associated only with that molecule.
• Dynamic Sets on page 214—Uses a rule to define membership.
Membership is determined when it is referenced, by interpreting the
expression in the context of the current molecular description. Both local
and global sets can exhibit dynamic properties.
• Built-in Sets on page 215—Always a dynamic global set and based on
properties or geometrical relationships which are subject to change. Can
be applied to atoms, bonds, or substructures.

SYBYL-X 2.1 SYBYL Basics 207

17. Sets in SYBYL

• Static Sets on page 220—Membership is identified at the time of set

definition.
• Aggregates—Local sets, always static, and user-defined. If defined by a
dynamic rule, it is immediately evaluated and membership becomes
static. Aggregates are recognized by the minimizer as groups of atoms
and bonds whose relative geometry is not to be optimized. (See the
discussion of Aggregates in the Force Field Manual for additional infor-
mation.)
• User-Defined Sets—Either dynamic (local or global) or static sets
created by the user. Global sets defined by the user are always dynamic
and are used exactly as those carried in the macromol dictionary. In
some cases, a set can be defined equally well as static or dynamic,
depending upon whether membership is likely to change during the
course of the project. For example:
• Alpha_helical region of a peptide.
• Chair and boat conformations of six-membered rings in a polycyclic
structure.
• Charge range for atoms carrying an electrostatic charge between the
values of 0.1 and 0.5 esu.

Additional Information:
• Working with Sets on page 221
• How to Use the Atom Expression Dialog on page 72 for examples of
how to use defined sets
• Definitions of SYBYL Objects on page 170

208 SYBYL Basics SYBYL-X 2.1

 17. Sets in SYBYL
Global Sets

17.1 Global Sets

Global sets are dynamic sets not directly associated with any specific molecule.
They may be defined at any time and can be applied to any molecule. They are
always of the dynamic type. By their very nature they cannot include specific
objects. Once applied to a particular molecule, they are copied to that
molecule’s set list and remain associated with it, unless explicitly deleted. For
example, the definition of POSITIVELY_CHARGED.

Global sets which are built into the program are typically defined in the
macromol dictionary. When the dictionary is opened, sets are available for use
automatically.

Additional Information:
General Description of the Expression Dialogs on page 64

17.1.1 Define a Global Set

DEFINE GLOBAL_SET object_type object_expr name comment

object_type Class of object to be members of set: ATOM, BOND or SUB-

STRUCTURE.
object_expr Set of objects of indicated class (evaluated only when set is
referenced).
name Name for set. Must be unique. First character must be alpha-
betic and a maximum of 30 additional characters must be
alphanumeric or underscores (_).
comment Arbitrary string associated with set.

17.1.2 Modify a Global Set

Menubar: Not accessible from the menubar.

Create/Modify MODIFY GLOBAL_SET COMMENT set_expr {comment}
Comment via • set_expr—Expression indicating set to modify.
Command: • comment—Descriptive string, may contain any
characters and be of arbitrary length. Use double
quotes when entering spaces or special characters.

SYBYL-X 2.1 SYBYL Basics 209

17. Sets in SYBYL
Global Sets

Change Defini- MODIFY GLOBAL_SET DEFINITION set_expr

tion via Com- {object_exp}
mand: • set_expr—Expression indicating set to modify.
• object_expr—Rule for determining membership of the
dynamic set.
Global sets must be dynamic, hence the definition must be
in terms of a general expression rather than specific mem-
bers. The class of objects selected by a global set cannot
be altered by this procedure, only the definition.

Note: If a global definition is modified, it is modified in all instances associated

with the molecules in memory. If the local (molecule-associated) copy is
modified, it is no longer considered related to the global definition from which
it was derived. In that case, modification of the global set of the same name
does not affect the local copy.

17.1.3 Delete a Global Set

REMOVE GLOBAL_SET set_expr

set_expr Expression indicating set to remove, may include the wild-

card character (*). For example, to remove both g1 and g2,
enter g* or the expression g1,g2.

Note: If a global definition is deleted, its copies associated with the molecules
in the work areas are also deleted. If the local (molecule-associated) copy is
modified, it is no longer considered related to the global definition from which
it was derived. In that case, deletion of the global set of the same name does not
affect the local copy.

17.1.4 Global Sets in the Biopolymer Dictionary

Although you can define a new global set as it becomes necessary, several
global sets are already associated with the macromol dictionary and automati-
cally become available for use when the dictionary is opened.

The table below provides a complete listing of global sets currently available in
the macromol dictionary, accompanied by objects to which they apply and a
defining expression explaining how the various sets were created.

Name Objects Defining Expression

ACIDIC Substs {MONTYPE(asp,glu,tyr)}

BASIC Substs {MONTYPE(his,arg,lys)}

210 SYBYL Basics SYBYL-X 2.1

 17. Sets in SYBYL
Global Sets

Name Objects Defining Expression

BLOCK Substs {MON-

TYPE(ace,nme,pyr,amd,for,nmt,nmm,cme,mes
,ees,boc)}
BULKY Substs {MONPROP(MOL_WT,140,9999)}
CALPHA Atoms CA
CAP Substs {MONTYPE(amn,cxl,ami,cxc)} for proteins
{MONTYPE(hb,he)} for DNA and RNA
DISULFIDE Bonds sg-cb-hg-lpg1-lpg2,sd-cg-hd-1pd1-1pd2
DNA Substs {MONTYPE(dA,dG,dC,dT)}
HYDROPHOBIC Substs {MONTYPE(gly,ala,ile,leu,met,phe,pro,
trp,val)}
MOD_AA Substs {MONTYPE(abu,aib,arz,asz,bal,cym,cyx,glz,
hcx,hcy,hid,hie,hip, hpr,hse,hyp,lyz,nle,nva,
orn,orz,phg,pse,psm,psz,ptm,pty,ptz)}
NEUTRAL Substs {MONTYPE(tyr,his,asn,cys,gln,ser,thr)} +
{HYDROPHOBIC}
POLAR Substs {MONTYPE(asp,glu,tyr,asn,gln,thr,ser,cys,
his,lys,arg)}
PURINE Substs {MONTYPE(dG,dA,rG,rA)}
PYRIMIDINE Substs {MONTYPE(dC,dT)} for DNA
{MONTYPE(rC,rU)} for RNA
RNA Substs {MONTYPE(rA,rG,rC,rU)}
STD_AA Substs {MONTYP(ala,arg,asp,asn,cys,glu,gln,gly,his,
ile,leu,lys,met,phe,pro,ser,thr,trp,tyr,val)}
SUGAR Substs {MONTYPE(glb,mab,maa,gaa,gab,frb,fra,dra,
drb,rba,rbb)}

Note: Atomic weights correlate with the latest accepted figures from IUPAC
and NIST. The average difference is 0.01% of the old values. In the cases of
unstable atoms, the values for the most stable isotope are used.
• IUPAC: Pure Appl. Chem. 2003, 75, 1107-1122
• National Institutes of Standards and Technology (NIST)

Additional Information:
• Dictionary Files description in the Biopolymer Manual

SYBYL-X 2.1 SYBYL Basics 211

17. Sets in SYBYL
Local Sets

17.2 Local Sets

A local set consists of objects in a particular molecule. Membership is
associated only with that molecule. Local sets may be defined by any user at
any time. Examples are the definition of a protein’s active site and aggregates
used during minimization.

Local sets may be dynamic or static.

• Dynamic Sets on page 214
• Static Sets on page 220

When an atom or a bond involved in a local set is removed from the molecule,
the set membership is automatically updated.

Additional Information:
General Description of the Expression Dialogs on page 64

17.2.1 Modify a Local Set

Menubar: Edit > Sets > Modify Set

Create/Modify MODIFY LOCAL_SET COMMENT set_expr {comment}
Comment via • set_expr—Expression indicating set to modify.
Command: • comment—Descriptive string, may contain any
characters and be of arbitrary length. Use double
quotes when entering spaces or special characters.
Change Defini- MODIFY LOCAL_SET DEFINITION set_expr
tion via Com- {object_expr [merge]}
mand: • set_expr—Expression indicating set to modify.
• object_expr—Membership (for a static set) or rule for
determining membership (for a dynamic set).
• merge—NO/YES, for static sets only, whether to add to
or replace current definition.
For dynamic sets, there is no merge option; they are com-
pletely redefined by this command.
Change Name via MODIFY LOCAL_SET NAME set_expr {name}
Command: • set_expr—Expression indicating set to modify.
• name—Name for set.
First character of set name must be alphabetic and may be
followed by up to 30 additional characters, including
alphabetic, numeric, and the underscore (_). Names must
be unique among all other (GLOBAL or LOCAL) sets and
also among substructures.

212 SYBYL Basics SYBYL-X 2.1

 17. Sets in SYBYL
Local Sets

17.2.2 Delete a Local Set

Delete a user-defined local set, static or dynamic, from a molecule’s
description.

Menubar: Edit > Sets > Delete Set

Command: REMOVE LOCAL_SET set_expr
• set_expr—Expression indicating the set(s) to remove,
may include wildcard character (*). For example, to
remove both s1 and s2, enter s* or the expression s1,s2.

SYBYL-X 2.1 SYBYL Basics 213

17. Sets in SYBYL
Dynamic Sets

17.3 Dynamic Sets

A dynamic set is a group of objects whose membership is evaluated dynami-
cally (only when the set name is used in a command or is referenced by an
application routine). A standard object expression is analyzed at the time of
reference to determine the current set of objects meeting the requirements of the
expression. The expression must be valid for the type of object the set is to
contain.

Because objects are not permanently assigned to a set of this type, dynamic sets
are most often used to monitor properties of molecules which are subject to
change, such as conformation, charge, strain energy among many others.

17.3.1 Define a Dynamic Set

Menubar: Edit > Sets > Create Dynamic Set

Command: DEFINE DYNAMIC_SET object_type object_expr
name comment
• object_type—Class of object to be members of the set:
ATOM, BOND or SUBSTRUCTURE.
• object_expr—Expression of objects, of indicated class, to
include in set (evaluated only when set is referenced).
• name—Unique name for set. First character must be
alphabetic with a maximum of 30 more characters (alpha-
numeric or underscores (_)).
• comment—Comment string.

17.3.2 Examples of Dynamic Sets

Define all substructures (monomers) within 10 Å of atom C1 in residue A17 as
members of the set called ACTIVE_SITE:
DEFINE DYNAMIC_SET SUBSTRUCTURE {SPHERE(A17.C1,10)} \
active_site “10Å radius around A17”
If the atoms are manipulated (e.g., conformations are modified), membership in
this set can change.

Color the atoms that are members of the dynamic set ACTIVE_SITE:
COLOR ATOM {active-site} MAGENTA
The membership is evaluated at the time of reference according to the definition
rule. Substructures belonging to the set are expanded into their constituent
atoms for the execution of the command.

214 SYBYL Basics SYBYL-X 2.1

 17. Sets in SYBYL
Built-in Sets

17.4 Built-in Sets

The membership of a built-in set is determined at the time it is referenced.
Built-in sets may not be created, removed, or altered by the user.

Built-in sets differ from the general dynamic set types:

• Evaluation rules are built into the program.
• They may require one or more arguments to direct their evaluation.
Required arguments are specified in parentheses after the set name,
separated with commas. For example, {SPHERE(C2,5)} specifies all
atoms within 5 Å of atom C2.

The table below describes the built-in sets currently available in SYBYL, the
forms in which they are invoked (commands and arguments required, if any),
explanations, and examples.

AROMATIC {AROMATIC(atom_expr)}
• Atoms Atoms in the same aromatic system as the specified
atom(s).
LIST ATOM {AROMATIC(9)} BRIEF
BACKBONE {BACKBONE}
• Atom Set Atoms belonging to the backbone as defined in the
macromol dictionary.
COLOR ATOM {BACKBONE} RED
• Bonds {BACKBONE}
Bonds belonging to the backbone as defined in the mac-
romol dictionary.
SCAN {BACKBONE}
BIOPOLYMER {BIOPOLYMER(option1,option2,…)}
• Substructure Substructures in a biopolymer. Options are:
• PROTEIN—Selects amino acids in protein chains
(including modified amino acids). It is similar to
{SEQUENCE(*)}
• DNA—Selects nucleic acids in DNA chains.
• RNA—Selects nucleic acids in RNA chains.
• COFACTOR—Selects cofactor substructures, as
defined in the biopolymer dictionaries.
• WATER—Selects water substructures, as defined in
the biopolymer dictionaries.
• LIGAND—Selects substructures not included in the
above categories and not a carbohydrate, as defined
in the biopolymer dictionaries. All members of the
{METAL} set are also excluded.
LIST SUBSTRUC {BIOPOLYMER(LIGAND)} FULL

SYBYL-X 2.1 SYBYL Basics 215

17. Sets in SYBYL
Built-in Sets

BUMPS {BUMPS(atom1,atom2)}
• Atoms Atoms in one group having van der Waals contacts with
atoms of the other group. van der Waals parameters
stored in the file $TA_ASCTABLES/ATOM_DEF are
used.
Use Tailor variable GENERAL BUMPS_CONTACT_DIS-
TANCE to define the cutoff distance. Negative values
allow overlap of van der Waals spheres, positive val-
ues prohibit it. Default is 0.0 Å.
COLOR ATOM {BUMPS(atom1,atom2)} MAGENTA
CHARGE {CHARGE(minimum,maximum)}
• Atoms Atoms having a residual charge in the specified range.
COLOR ATOM {CHARGE(-.05,-.01)} BLUE
CHIRAL {CHIRAL(atom_expr,RS)}
• Atoms Atoms of the specified chirality or pro-chirality. Spec-
ify the atoms to search as an expression. Chirality is
indicated by the second argument as: R, S, RS, PRO_R,
PRO_S, or PRO_RS. If RS or PRO_RS is entered, all cen-
ters are included in the set. The default is to search all
atoms (*) for all chiral centers (RS).
COLOR ATOM {CHIRAL(CA,S)} YELLOW
FINDCONF {FINDCONF(state1+state2+,sequence)}
• Substructures Monomers having the specified conformational state(s)
as defined in the macromol dictionary. Entering a
sequence limits the search to the specified regions of
the biopolymer (“*” searches whole biopolymer). Sepa-
rate conformational states by plus signs.
LABEL SUBSTRUCTURE {FINDCONF(ALPHA_
HELIX,*)}
H_CONN_VIS_HEV {H_CONN_VIS_HEV(atom_expr,type)}
Hydrogen atoms that are connected to visible heavy
atoms. Valid types include: ALL, HBOND, NONHBOND,
POLAR, or NONPOLAR. It is used to display hydrogens in
the Protein View and in the Molecule Display Options
tools.
HBOND {HBOND(atom_expr,type)}
• Atoms Atoms of the specified type participating in hydrogen
bonds. Valid types include: ALL, DONOR, ACCEPTOR, or
HYDROGEN. Definitions for the donor and acceptor
atoms are in the parameter table $TA_ASCTABLES/
ATOM_DEF as H_ACCEPTOR and H_DONOR fields.
LIST ATOM {HBOND(1+2+3+4+5+6,donor)}
BRIEF

216 SYBYL Basics SYBYL-X 2.1

 17. Sets in SYBYL
Built-in Sets

METAL {METAL}
• Atoms Atoms with a metallic ordinal number (according to the
periodic table). This set also includes metal atoms in
cofactors.
COLOR ATOM {METAL} PURPLE
MONPROP {MONPROP(keyword,minimum,maximum)}
• Substructures Monomers having the specified property as identified
by a keyword and (optional) minimum and maximum
values. Enter only the keyword to select all monomers
having that keyword. Enter the keyword and a mini-
mum to select monomers with the keyword whose
value matches the minimum. The keyword may be any
arbitrary string. Values may be real, integer, or string.
Properties are stored in the macromol dictionary
(molecular weight is stored as MOL_WT).
LABEL SUBSTRUCTURE {MONPROP(MOL_
WT,150,200)}
MONTYPE {MONTYPE(type1,type2,...)}
• Substructures Monomers of the specified type(s). Types are defined
in the macromol dictionary. As many types as desired
may be specified as arguments. An asterisk (*) speci-
fies all substructures that are monomers.
LABEL SUBSTRUCTURE {MONTYPE(A,T)}
POSSIBLE_HBOND {POSSIBLE_HBOND(atom_expr,type)}
• Atoms Atoms of the specified type which can potentially par-
ticipate in hydrogen bonds. Valid types include:
• ALL
• DONOR—Potential H bond donor atom, attached to a
hydrogen or has at least one free valence.
• ACCEPTOR—Potential H bond acceptor.
• HYDROGEN—Hydrogen attached to an H bond
donor.
LIST ATOM {POSSIBLE_HBOND(*,all)} BRIEF
RINGS {RINGS(atom_expr,type)}
• Atoms Specified atoms which are included in rings of the
specified type. Types include:
• I—Internal rings (completely contained within a
substructure).
• E—External rings (crossing substructure bound-
aries).
• EI (IE)—Either internal or external.
If no arguments are entered, defaults to
{rings(*,EI)}.
COLOR ATOM {RINGS(*,E)} BLUE

SYBYL-X 2.1 SYBYL Basics 217

17. Sets in SYBYL
Built-in Sets

• Bonds {RINGS(bond_expr,type)}
Specified bonds which are included in rings of the
specified type. Types include:
• I—Internal rings (completely contained within a
substructure)
• E—External rings (crossing substructure bound-
aries)
• EI (IE)—Either internal or external.
If no arguments are entered, defaults to
{rings(*,EI)}.
COLOR BOND {RINGS(*,I)} RED
• Substructures {RINGS(substructure_expr,type)}
Substructures in the expression, which are included in
rings of the specified type.
LABEL SUBSTRUCTURE {RINGS(*,E)}
SEQUENCE {SEQUENCE(sequence1,sequence2,)}
• Atoms Atoms in monomers of the specified sequence(s).
Monomers are defined in the macromol dictionary. See
Specific Monomer Sequences (in the SPL Manual) for
more information.
COLOR ATOM {SEQUENCE(GLY=PRO,GLY=GLY)}
BLUE
COLOR ATOM {SEQUENCE(A/1:25)} RED
COLOR ATOM {SEQUENCE(<,>)} MAGENTA
• Bonds {SEQUENCE(sequence1,sequence2,)}
Bonds in monomers of the specified sequence(s).
Monomers are defined in the macromol dictionary.
SCAN {SEQUENCE(GLY=PRO)}
• Substructures {SEQUENCE(sequence1,sequence2,)}
Monomers in the specified sequence(s). Monomers are
defined in the macromol dictionary.
LABEL SUBSTRUCTURE
{SEQUENCE(A=T=C,T=*=U)}
SIDECHAIN {SIDECHAIN}
• Atoms Atoms belonging to sidechains as defined in the macro-
mol dictionary. Only sidechains attached to the
biopolymer backbone are considered.
COLOR ATOM {SIDECHAIN} RED
• Bonds {SIDECHAIN}
Bonds belonging to sidechains as defined in the macro-
mol dictionary. Only sidechains attached to the
biopolymer backbone are considered.
SCAN {SIDECHAIN}

218 SYBYL Basics SYBYL-X 2.1

 17. Sets in SYBYL
Built-in Sets

SPHERE {SPHERE(atom_expr,radius)}
• Atoms Atoms falling within sphere(s) of the specified radius.
The expression defines the sphere center(s). When mul-
tiple atoms are selected, the final set is the union of sets
of atoms within spheres of indicated radius about each
center. All spheres have the same radius.
COLOR ATOM {SPHERE(ALA23.CA,10)} MAGENTA
• Bonds {SPHERE(atom_expr,radius)}
Bonds falling within sphere(s) of the specified radius.
The expression defines the sphere center(s). When mul-
tiple atoms are selected, the final set is the union of sets
of bonds within spheres of indicated radius about each
center. Note: Only bonds with both endpoint atoms in
the sphere are accepted. All spheres have the same
radius.
SCAN {SPHERE(N15,8)}
• Substructures {SPHERE(atom_expr,radius)}
Substructures falling within sphere(s) of the specified
radius. The expression defines the sphere center(s).
When multiple atoms are selected, the final set is the
union of sets of substructures within spheres of indi-
cated radius about each center. Note: Substructure is
accepted, even if only one of its atoms falls within the
sphere. All spheres have the same radius.
LABEL SUBSTRUCTURE {SPHERE(G16,12)}
SUBST_SPHERE {SUBST_SPHERE(atom_expr,radius)}
Atoms, bonds, or substructures falling within sphere(s)
of the specified radius. For atoms and bonds the
returned list is expanded to complete substructures. The
expression defines the sphere center(s). When multiple
atoms are selected, the final SUBST_SPHERE set is the
union of sets of substructures included in spheres of
indicated radius about each center. Note: Substructure
is accepted, even if only one of its atoms falls within
the sphere (identical to SPHERE for substructures).
TO_ATOMS {TO_ATOMS(atom_expr)}
• Bonds Bonds with one or both atoms in the atom expression.
SCAN {TO_ATOMS(CA)} CYAN

Additional Information:
• SYBYL Atom Types in the Force Field Manual
• Global Sets in the Biopolymer Dictionary on page 210
• General Description of the Expression Dialogs on page 64

SYBYL-X 2.1 SYBYL Basics 219

17. Sets in SYBYL
Static Sets

17.5 Static Sets

Membership of a static set is determined by a standard object expression
analyzed at the time of definition. Once specified, this membership does not
change unless one of the elements is deleted from the molecule. In this case, it
is automatically removed from the set as well and the membership is redefined.
With the exception of set members deleted from the molecule, every time you
reference a static set, the same elements are selected. Only local sets can have
static properties.

The latitude with which you can define members of a static set provides great
flexibility in the manipulation of molecular data. For example, static sets can
define:
• Active site portion of an enzyme (select atoms or monomers involved)
• Diene and dienophile portions of a molecule designed to undergo an
intramolecular cyclo-addition reaction
• Glycone and aglycone portions of a nucleoside
• Acyclic precursor region of what becomes part of a larger structure upon
cyclization

In addition, in SYBYL’s Biopolymer program, static sets are automatically

generated when molecules are read in from Protein Data Bank files.

17.5.1 Define a Static Set

Menubar: Edit > Sets > Create Static Set

Command: DEFINE STATIC_SET object_type object_expr
name comment
• object_type—Class of object to be members of set:
ATOM, BOND or SUBSTRUCTURE.
• object_expr—Expression of objects, of indicated class,
to include in set. object_expr is not retained with set
definition.
• name—Unique name for set. First character must be
alphabetic with a maximum of 30 additional characters
(alphanumeric or underscores (_)). Default is the
current name plus and underscore and number.
• comment—Comment string. If you modify the set, the
default comment is the current comment plus _new.

220 SYBYL Basics SYBYL-X 2.1

 17. Sets in SYBYL
Working with Sets

17.6 Working with Sets

When you modify, list, or remove sets, SYBYL displays a dialog containing the
defined sets. Click the molecule in the list and use the selection tools to specify
the desired sets to modify, list, or remove. Highlighting a set in the list also
highlights the atoms in that set in the SYBYL window.

The examples below show the dialogs invoked for a protein.

Options > List > Sets Options > List > Global Sets

Select a molecule: Select the molecule area and molecule from the list.
Buttons to assist in the selection of sets: select all, invert
selection, clear selection.

SYBYL-X 2.1 SYBYL Basics 221

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18. Libraries of Fragments and Functional Groups

SYBYL includes libraries of chemical fragments and functional groups that can
be used to build small molecules.

Both libraries are in $TA_DATA.

In this section, you will find:

• Fragment Library on page 224
• Load Fragments from the Library on page 224
• Structure and Contents of the Fragment Library on page 226
• Group Library on page 229
• Add a Functional Group to a Structure on page 229
• Structure and Contents of the Group Library on page 229

SYBYL-X 2.1 SYBYL Basics 223

18. Libraries of Fragments and Functional Groups
Fragment Library

18.1 Fragment Library

18.1.1 Load Fragments from the Library
SYBYL provides a library of fragments from which you can easily build small
molecules.

Load a Single Fragment by Name

Menubar: File > Get Fragment

• Select one fragment in the list.
The fragment will be loaded into the first empty mole-
cule area.
Command: FRAGMENT NAME name mol_area
• name—Name (with optional wildcards) of the
fragment to retrieve.
• mol_area—Area to receive the fragment.
For example, FRAGMENT NAME BENZENE M1 retrieves
the fragment BENZENE into M1.
FRAGMENT NAME VIT*B2 M1 retrieves the fragment
Vitamin B2 into M1 (because only one fragment satis-
fies the expression VIT*B2).

224 SYBYL Basics SYBYL-X 2.1

 18. Libraries of Fragments and Functional Groups
Fragment Library

Load Multiple Fragments by Name

Command: FRAGMENT NAME name_expr

[QUIT|RETRIEVE|SELECT|UNSELECT]
• name_expr—Name (with optional wildcards) speci-
fying multiple fragments to retrieve.
If no fragment is found or a if single fragment is
retrieved, no further input necessary (i.e., entering one
of the following items is skipped).
• QUIT—Exit search procedure without choosing a
molecule.
• RETRIEVE [mol_area]—Retrieve multiple
fragments starting with specified mol_area.
• SELECT [name_expr]—Select subset of currently
chosen molecules according to their names.
• UNSELECT—Unselect list of fragments. This undoes
previous SELECT operation, thus allowing a more
flexible search of the library. It can be applied any
number of times.
For example, FRAGMENT NAME BE* RETRIEVE M1
retrieves all fragments starting with the letters BE and
places them in consecutive molecule areas starting with
M1.

Use the Menu to Retrieve a Fragment

Command: FRAGMENT MENU menu_choices mol_area

• menu_choices—Series of numbers, typed at the
keyboard, identifying successive menu items.
• mol_area—Area to receive selected fragment,
current contents are overwritten.
Menus are hierarchical and categorize various molecu-
lar fragments according to structure and/or function.
Enter numbers to move down the hierarchy until
desired molecule is found. Typing the number of an
actual molecule retrieves that molecule.
Three words can also be used:
• TOP—Return to top level of menu hierarchy, where
the most general categories are displayed.
• UP—Back up one level in the hierarchy to a set of
more general categories.
• QUIT—Exit from search procedure without
choosing a molecule.

SYBYL-X 2.1 SYBYL Basics 225

18. Libraries of Fragments and Functional Groups
Fragment Library

Additional Information:
• Libraries of Fragments and Functional Groups on page 223
• Load a Molecule from the Fragment Library on page 16

18.1.2 Structure and Contents of the Fragment Library

As supplied by Tripos, the fragment library contains approximately 200 small
molecules (fragments) that can be used to build organic molecules with good
initial geometries. Each fragment is the result of averaged crystallographic
observations (i.e., averaged geometries from the Cambridge data file).

Access:
• File > Get Fragment — Retrieve a fragment by name.
• FRAGMENT — Retrieve a fragment by name or through a menu selection.

The library is organized in a hierarchical fashion. This hierarchy is accessible

only in the console via the FRAGMENT MENU command.

One of the high-level categories in the hierarchy is “Cyclic Systems”—clearly a

very general grouping. From this category you may descend to heterocyclic
systems with two rings, then to those with one heteroatom, then to 56 ring
systems. At this point you reach the lowest level categories, those consisting
actual molecules where, in this case, you would find indole or benzofuran.

226 SYBYL Basics SYBYL-X 2.1

 18. Libraries of Fragments and Functional Groups
Fragment Library

The lowest level groups—those which contain the actual molecules—are static
sets, while all higher level categories are dynamic classes, defined as the union
of those groups directly under them. Thus the “56 Systems” are contained in a
static set, such as FIVESIX, but the group which corresponds to “1 Heteroatom”
in the above diagram is a dynamic class defined as the union of FIVESIX and
SIXSIX (FIVESIX+SIXSIX). Similarly, “Heterocyclic 2 Rings” is a dynamic
class defined as the union of “1 Heteroatom”, “2 Heteroatoms” and “>2
Heteroatoms”.

Tripos’ standard fragment library contains about 200 molecules partitioned into
44 static sets, and categorized into a hierarchy comprised of 17 dynamic classes.
Below is the full listing of sets and classes provided by Tripos to organize the
fragment library. In the listing, the dynamic classes are represented in italic
script, all others are static sets.

A: Acyclic Functions
• AA: Carbon Only
• AB: Function N
• AC: Function O
• AD: Function S
• AE: Function NO
• AF: Function SO
• AG: Function PO
• AH: Other
B: Cyclic Functions
• BA: Homocyclic, 1 Ring
BAA: Saturated
BAB: Unsaturated, 1 Double Bond
BAC: Unsaturated, 2 Double Bonds
BAD: Unsaturated, >2 Double Bonds
BAE: Aromatic
• BB: Homocyclic, 2 Rings
BBA: Saturated
BBB: Unsaturated
• BC: Homocyclic, 3 Rings
• BD: Homocyclic, 4 Rings
BDA: Steroids
BDB: Other
• BE: Heterocyclic, 1 Ring

SYBYL-X 2.1 SYBYL Basics 227

18. Libraries of Fragments and Functional Groups
Fragment Library

BEA: 1 Heteroatom
• BEAA: 5 Membered Ring, Saturated
• BEAB: 5 Membered Ring, Unsaturated
• BEAC: 6 Membered Ring, Saturated
• BEAD: 6 Membered Ring, Unsaturated
• BEAE: Other
BEB: 2 Heteroatoms
• BEBA: 5 Membered Ring, Saturated
• BEBB: 5 Membered Ring, Unsaturated
• BEBC: 6 Membered Ring, Saturated
• BEBD: 6 Membered Ring, Unsaturated
BEC: >2 Heteroatoms

• BF: Heterocyclic, 2 Rings

BFA: 1 Heteroatom
• BFAA: 56 Systems
• BFAB: 66 Systems
BFB: 2 Heteroatoms
• BFBA: 56 Systems
• BFBB: 66 Systems
BFC: >2 Heteroatoms
• BG: Heterocyclic, 3 Rings
BGA: 1 Heteroatom
• BGAA: 656 Systems
• BGAB: 666 Systems
• BGAC: 676 Systems
BGB: 2 Heteroatoms
• BGBA: 666 Systems
• BGBB: 676 Systems
BGC: >2 Heteroatoms
C: Amino Acids
D: Nucleic Acids
• DA: Bases
• DB: Ribose Monophosphate
E: Biologically Important Molecules
• EA: Vitamins
• EB: Sugars
• EC: Lipids

228 SYBYL Basics SYBYL-X 2.1

 18. Libraries of Fragments and Functional Groups
Group Library

18.2 Group Library

18.2.1 Add a Functional Group to a Structure
You can add a functional group to the molecular structure and have their
geometry determined from the parameter tables. The atoms in the group and
their relative positions are read from the Group Library.

Menubar: Not accessible from the menubar.

Command: ADD GROUP group_name ATTACH | REPLACE atom
• group_name—Name of group to add to structure. (Type
“?” at prompt to list available groups.)
• ATTACH—Add new group to specified atom with appro-
priate geometry.
• REPLACE—Remove specified atom and add new group
in its place, with ideal geometry (useful when
hydrogens are present).
• atom—Atom for attachment or to replace.

18.2.2 Structure and Contents of the Group Library

As supplied by Tripos, the group library contains a variety of small functional
groups frequently used in the construction of molecules. Each group has a
predefined attachment point.

ALLYL AMIDE BENZYL

CN CO CO2
CO2MINUS CS CYCLOHEXYL
EPOXY ETHYL ISOPROPYL
N-AMIDE N-BUTYL N-N
N-PROPYL N3 N=N
NH2 NO NO2
OCO OH ONO
OO PHENYL SEC-BUTYL
SH SO SO2
SO2N SO2O T-BUTYL
VINYL

Additional Information:
Sketcher Toolbars on page 105

SYBYL-X 2.1 SYBYL Basics 229

This page intentionally blank.
 SYBYL Basics Index

A B
Abort a console command 33 Backbone built-in set 215
Acidic global set 210 Basic global set 210
Add Benchware 3D Explorer
atoms 136 read/write file 46
bond 148 Bibliography
chain of atoms 137 Shake algorithm 158
chemical group 229
hydrogens 138 Biopolymer
pseudo-atoms 137 built-in set 215
standalone atom 136 global sets 210

Aggregate, local static set 208 Block global set 211

Alternate atom types 142, 143 Bond

add 148
Amino acid global sets 211 definition of types 68
Angle delete 150
between planes 155 list bond lengths 156
measure 154 modify type 151
modify 157 select 57
Aromatic built-in set 215 SYBYL object definition 170
Atom Bond expression dialog 64
add 136 Build
copy 110 sketch small molecule 101
delete 139 Built-in sets 215
list coordinates 156
merge 112 Bulky global set 211
modify 141 Bumps built-in set 216
modify coordinates 145
move 111
renumber 145 C
select 57 C-alpha carbon global set 211
SYBYL object definition 170
Cap global set 211
Atom expression dialog 64
CAPTURE command 204
Atom types
Center of mass 159
alternate set 142, 143
modify 141 Centroid 160
Attributes Charge
charge built-in set 216
remove from atoms 140 modify 144
set on atom 144 Chiral built-in set 216
stereochemistry
CHIRAL command 125
mark on atoms 125
mark on bonds 125 Chirality
remove from atoms 127, 140 check 99
remove from bonds 127, 150 determine and modify 125
invert 126
Automatic command execution 26
Class, define in a database 188
AVERAGE_MOL command 122
Clear the screen 85
Collect commands into a file 202

SYBYL-X 2.1 SYBYL Basics 231

Command console 32 plane 163
Command mode static set 220
special characters 33 UNITY features 166

Conformation, scan torsions 158 Delete

atoms 139
COPY command 110 bond 150
Copy molecule area contents 110 center of mass 160
Customize SYBYL start up 26 centroid 161
connected atoms 140
extension point 162
D global set 210
hydrogens 140
Database
line 162
add molecules 187
local set 213
classes 188
molecule 86
close 181
molecule in a database 188
copy contents to new database 181
non query atoms 167
copy database directories 194
normal 165
create empty database 180
plane 163
define alias 181
substructure 132
define class or set 189
SYBYL session 200
delete 188
UNITY feature 167
deleting database directories 194
get a molecule 182 Display area 55
grouping mechanisms 188 Distance
list measure 154
contents of open database 186 modify 157
molecule and group information 186
Disulfide global set 211
open databases 186
open 179 DNA global set 211
rename molecules 189 Dynamic set 214
reorganize contents 190 (see also Local sets)
save as 187 SYBYL object definition 173
save to Mol2 file 191
search 183
sets 188 E
show status 186 Environment variable
specify default database 181 SAVE_SESSION_DIR 196
view as a spreadsheet 185 TA_HIDE_UNLICENSED_PRODS 28
DATABASE command 193 Export molecule 35
dbtranslate utility Extension point 161
dialog 49
options 50 External ring
see UNITY manual SYBYL object definition 172

Default molecule area 56 EXTRACT command 111

Define
center of mass 159 F
centroid 160
Features
dynamic set 214
center of mass 159
extension point 161
centroid 160
global set 209
extension point 161
line 162
line 162
normal 164

232 SYBYL Basics SYBYL-X 2.1

 normal 164 special characters 33
plane 163 Hide menu options 28
SYBYL object definition 171
UNITY 166 Hydrogens
add 138
File formats delete 140
convert between molecular formats 49
Hydrophobic
File selection dialog 36 global set 211
Files
convert between molecular formats 49
read/write I
Benchware 3D Explorer files 46 Import molecule 35
MDL Mol file 43
Information
SD file 43
report on atom, bond, or substructure 174
SLN 43
Internal ring
Files created
SYBYL object definition 172
capture the output of a command 204
COLLECT 202 Invert chirality 126
Mol2 40
record the console dialogue 205
J
Fill valences 138
Job control console 32
Findconf built-in set 216
JOIN command 116
FRAGMENT command 224
Join groups or molecules 116
Fragment library 224
structure and contents 226 Journal
collect console commands 202
FUSE command 116 PHOTO command 205
Fuse ring 116
tutorial 117
K
Kollman atom types 142, 143
G
Geometry
measure 154 L
modify 157 Libraries 223
Global sets 209 License requirements
for biopolymers 210 SYBYL basics 9
Grid Line feature 162
SKETCH 107
List
Group library 229 atom coordinates 156
add 229 bond angles 156
SKETCH 105 bond lengths 156
structure and contents 229 non-bonded distances 156
object information 175
torsion angles 156
H
Load molecule 16
H_CONN_VIS_HEV built-in set 216 commands 42
Hbond built-in set 216 fragment library 16
Height measurement 154 Local set 212
Help 21 Lone pair

SYBYL-X 2.1 SYBYL Basics 233

 MODIFY 145 delete 86, 123
delete in a database 188
evaluating features 159
M extract atoms 111
MDL Mol file merge 112
convert to molecular spreadsheet 46 modify 109, 128, 135
convert to SLN file 46 modify name 124
read/write 43 read files 35, 36
rotate, translate, scale 17
MDLMOL command 43
save 40
Measure save as 20
angle 154 save in a database 187
distance 154 select 57
height 154 split 140
plane angle 155 type 128
torsion 155 write files 35, 36
UNITY features 155
Molecule area
Menubar 28 default 56
shortcuts 29 rules 55
Merge SYBYL object definition 170
atoms 113 Molecule expression dialog 71
exceptions 113
Monprop built-in set 217
merging features 113
non-unique atom 114 Montype built-in set 217
structures 113
unique atom 113
N
MERGE command 112
Name
Metal built-in set 217 atom
Modified amino acid global set 211 modify 144
Modify local set 212
angle 157 Neutral global set 211
atom 141 Normal ro a plane 164
bond 151
distance 157 Notebook
global set 209 collect console commands 202
local set 212 PHOTO command 205
molecule 128
molecule name 124 O
substructure 131
substructure name 133 Object definitions 170
torsion 157 Open molecule file 36
UNITY feature 167
Open saved SYBYL session 200
Mol2 file, read/write 42
Molecular Spreadsheet
MDL Mol file conversion 46
P
Molecule PHOTO command 205
average 122 Plane 163
build 109, 112, 135 measure angle 155
combine 112 reflect through 126
copy 110 Play back session
defining features 159 COLLECT and TAKE files 202

234 SYBYL Basics SYBYL-X 2.1

 command file 203 SCAN command 158
Polar global set 211 SD file, read/write 43
Possible_hbond built-in set 217 Select objects 57
Print information to a file 176 Sequence built-in set 218
Purine global set 211 Sequence expression dialog 64
Pyrimidine global set 211 Session
delete 200
Manage 195
Q new 201
Query expressions 183 open saved session 200
restore 200
QUICKBOND command 148
save 196
SESSION command 195
R Sets 207
Read molecule 35 aggregates 208
fragment library 16 built-in 215
Read/save database molecules 191 database 188
dynamic 214
Record for biopolymers 210
console commands 202 global 209
Recover contents of molecule area 91 local 212
References static 220
Shake algorithm 158 SYBYL object definition 172
user-defined 208
Reflect atoms through a plane 126 working with 221
RENUMBER command 145 SHAKED command 158
Reset the screen 85 Shortcuts
Restore dialogs 29
SYBYL session 200 keyboard 34
undo the last operation 91 menubar 29
Retrieve molecules 182 mouse 29

Ring Sidechain built-in set 218

built-in set 217 Sketcher 101
fusion 116 add Z coordinate 104
list 175 branching 103
ring fusion tutorial 117 change atom types 102
SYBYL object definition 172 check chirality 99
RNA global set 211 draw a ring 104
draw multiple bonds 103
Root atom 128 move an atom 106
techniques 101
S toolbar items 105
tutorial 94
Save
SLN
molecule in a file 35
read/write file 43
molecules 40
in a database 187 SLN typer 143
selected molecule(s) 40 Small molecule building 101
SYBYL session 196
Sphere built-in set 219
SAVE_SESSION_DIR 196

SYBYL-X 2.1 SYBYL Basics 235

Spiro fusion 117 angle 154
Split molecule 140 collect file 203
database name 180, 181
Standard amino acids global set 211 distance 154
Start SYBYL 12, 27 height 154
Static set 220 photo file 205
define 220 plane angle 155
SYBYL object definition 172 torsion 154

Store molecules 187 Undo last action 91

Subst_sphere built-in set 219 UNITY

define features 166
Substructure delete
delete 132 features and constraints 167
modify 131 non query atoms 167
modify name 133 modify feature 167
root 133
selecting 57 User-defined sets 208
SYBYL object definition 170
type 134 Z
Substructure expression dialog 64
ZAP command 86, 123
Sugar global set 211

T
TAKE command 203
Tear-off menus 28
TMPDIR environment variable 190
To_atoms built-in set 219
Toolbar overview 31
Topography, list of coordinates and distance and an-
gles 156
Torsion
measure 155
modify 157
Translate molecular files 49
Tripos Bookshelf 21
TTY command 204
Tutorials
atom selection 72
bond selection 79
building a small molecule 94
ring fusion 117
sketching a small molecule 94
small molecule sketching 94
substructure selection 82

U
UIMS2 variables

236 SYBYL Basics SYBYL-X 2.1