PyMOL QuickRef 0905
PyMOL QuickRef 0905
Supplemental information intended for users who are already comfortable using PyMOL for basic molecular visualization
MOUSE
GRID
given atom.
Clip : Move clipping planes
Menu
Move
MovZ
Rota
Pk1
PkAt
Sele
Orig
+/-
+Box
-Box
Corner Buttons
S
defined Scenes.
[Ctrl-Page-Down] & [Ctrl-Page-Up] define a new Scene before or
discrete molecule.
Rot_ : Free rotation.
Mov_ : Move in XY plane.
MvZ_ : Move along Z axis.
_ above is A, D, F, or O:
A for atom
D for dragged selection
F for fragment
O for object
PkTB : Pick and (optionally) drag
Named selections save time by helping you refer back to specific atoms.
PyMOL> select binding_site, byres organic expand 5
PyMOL> show surface, binding_site
PyMOL> color cyan, binding_site and elem C
Selection Macros are a concise way of identifying atoms based on matching
identifier fields separated by slashes. They come in two forms...
Fields in macros with a leading slash are matched left-to-right:
/object/segi/chain/resn`resi/name`alt
/1hpv
/1dn2/B/B/`271
/1t46//A/LEU/CA
;# /object
;# /object/segi/chain/`resi
;# /object//chain/resn/name
;#
;#
;#
;#
;#
;#
;#
resi/name`alt
resi/name
resi/name
resn`resi/
chain/resi/
chain//
object/segi/chain/resn/
Often-used settings, configured via: set setting_name = setting_value and unset setting_name
opaque_background = off (transparent) vs. = on (opaque - default)
transparency = 0.5 (for surfaces; also set sphere_transparency, cartoon.., stick..., etc.)
transparency_mode = 1 (multi-layer) vs. = 2 (uni-layer - default )
ray_transparency_oblique = 1.5 (varies transparency based on surface normal)
surface_mode = 1 (surface all atoms) vs. = 0 (do not surface HETATMs - default)
surface_quality = 1 (higher quality) vs. = 0 (default)
surface_color = white (or other predefined color)
Commands scripts (.pml files) can include Python code three ways:
(#1) Implicitly, based on default Python fall-through handler:
load $PYMOL_PATH/test/dat/pept.pdb ;# PyMOL
;# Python
import os
print os.environ[PYMOL_PATH]
;# Python
(#2) explicitly on a single line with a leading forward slash (/) (with optional \ continuation lines ):
/a=4; b=5; print a+b \
print a-b
or (#3) explicitly in the form of embedded Python blocks with standard block indentation.
# a simple XYZ file reader
python
;# start of Python block
for line in open("example.xyz").readlines():
field = line.strip().split()
if len(field)==4:
xyz = map(float, field[1:4])
cmd.pseudoatom("my_example",elem=field[0], pos=xyz)
python end
;# end of Python block
show spheres, my_example
zoom
Copyrighted Material - Licensed for Use by PyMOL Sponsors Only - Unauthorized Reproduction Prohibited.
Each frame can have a camera waypoint stored with it, and can be interpolated for in-between frames with stored views
PyMOL> mview store,1; turn y,30; mview store,10; turn y,-30; mview store, 20
0
PyMOL> mview interpolate
;# do interpolation for missing frames
PyMOL> mview reinterpolate ;# redo interpolation for entire movie
mode = 1)
Objects can also be animated with mview using the object= optional argument (works best when matrix_mode
r; zoom
PyMOL> delete all; mset 1 x60; set matrix_mode=1; fragment lys; fragment tyr;
lys; mview store,object=lys
PyMOL> frame 1; mview store,object=lys; frame 30; translate [5,0,0],object=lys;
PyMOL> mview interpolate,object=lys
PyMOL> frame 1; mview store,object=tyr; frame 45; rotate
x, 90, object=tyr; mview store,object=tyr
PyMOL> mview interpolate,object=tyr
Movie commands can perform arbitrary actions on a per-frame basis (for a given frame, mdo resets existing commands , mappend doesnt).
PyMOL> mdo 1: show_as lines
PyMOL> mdo 30: show_as sticks
Also see: Movie menu program options, and
File menu Save As MPEG or individual PNG files.
Other types of alignment tasks can be performed with the following set of commmands:
super mobile, target
;# structure-based alignment which refines just like align
pair_fit mobile, target
;# atom-pair-based alignment, example: PyMOL> pair_fit obj1/2-7/CA, obj2/4-9/CA
fit mobile, target
;# identifier-based alignment, where all atom identifiers match
intra_fit selection
;# molecular-state-based alignment within a single molecular object
matrix_copy source_name, target_name
;# copies matrix from one object to another
Fragments
Fragment
Picked Atom
Joints
Fragments
Fragment
Right-click-and-drag to reorder.
http://pymolwiki.org
http://pymol.org/archive
http://delsci.info
Copyright 2009 DeLano Scientific LLC, 540 University Ave., Suite 325, Palo Alto, California, 94301-1928, U.S.A. All Rights Reserved.
Licensed for Use by PyMOL Sponsors Only - Unauthorized Reproduction Prohibited - Contact [email protected] for details (rev. 090513).