Pymol Reference Card

Modes
Pymol supports two modes of input: point and click mode,
and command line mode. The point and click allows you to
quickly rotate the molecule(s) zoom in and out and change
the clipping planes. The command line mode where commands are entered into the external GUI window supports
all of the commands in the point and click mode, but is
more flexible and possibly useful for complex selection and
command issuing. Commands entered on the command
line are executed when you press the return key.
command help
help keyword

Loading Files
file loading
load data/test/pept.pdb
loading from terminal
pymol data/test/pept.pdb
toggle between text and graphics
Esc
toggle Y axis rocking
rock
stereo view
stereo on/off
stereo type stereo crosseye / walleye / quadbuffer
undo action
undo
reset view
reset
reinitialize Pymol
reinitialize
quit (force, even if unsaved)
quit

Mouse Control
L
M
Rota
Move
Shift
+Box -Box
Ctrl
+/PkAt
CtSh
Sele
Cent
DblClk Menu Cent
set the center of rotation

Basic Commands

Image Output

Some commands used with atoms selections. If you are

unsure about the selection, click on the molecule part that
you want in the viewing window and then look at the output line to see the selection.

low resolution
high resolution
ultra-high resolution
change the default size [pts]
image shadow control
image fog control
image depth cue control
image antialiasing control
export image as .png

fill viewer with selection

zoom /pept//a
center a selection
center /pept//a
colour a selection
colour pink, /pept//a
force Pymol to reapply colours
recolor
set background colour
bg color white
vdW representation of selection show spheres, 156/ca
stick representation of selection
show sticks, a//
line representation of selection
show lines, /pept
ribbon representation of selection
show ribbon, /pept
dot representation of selection
show dots, /pept
mesh representation of selection
show mesh, /pept
surface representation of selection show surface, /pept
nonbonded representation of selection show nonbonded,
/pept
nonbonded sphere representation of selection
show
nb spheres, /pept
cartoon representation of selection
show cartoon, a//
clear all
hide all
rotate a selection
rotate axis, angle, selection
translate a selection
translate [x,y,z], selection

Cartoon Settings
R
MovZ
Clip
Pk1
Menu
PkAt

Wheel
Slab
MovS

origin selection

Atom Selection
object-name/segi-id/chain-id/resi-id/name-id
molecular system selection
/pept
molecule selection
/pept/lig
chain selection
/pept/lig/a
residue selection
/pept/lig/a/10
atom
/pept/lig/a/10/ca
ranges
lig/a/10-12/ca
ranges
a/6+8/c+o
missing selections
/pept//a
naming a selection
select bb, name c+o+n+ca
count atoms in a selection
count atoms bb
remove atoms from a selection
remove resi 5
general all, none, hydro, hetatm, visible, present
atoms not in a selection
select sidechains, ! bb
atoms with a vdW gap < 3
A
resi 6 around 3
atom centers with a gap < 1.0
A all near 1 of resi 6
atom centers within < 4.0
A
all within 4 of resi 6

Setting the value at the end to 0 forces the secondary structure to go though the CA position.
cylindrical helices set cartoon cylindrical helices,1
fancy helices [tubular edge]
set
cartoon fancy helices,1
flat sheets
set cartoon flat sheets,1
smooth loops
set cartoon smooth loops,1
find rings for cartoon
set
cartoon ring finder,[1,2,3,4]
ring mode
set cartoon ring mode,[1,2,3]
nucleic acid mode set nucleic acid mode,[0,1,2,3,4]
cartoon sidechains
set cartoon side chain helper;
rebuild
primary colour
set cartoon color,blue
secondary colour
set cartoon highlight color,grey
limit colour to ss
set cartoon discrete colors,on
cartoon transparency
set cartoon transparency,0.5
cartoon loop
cartoon loop, a//
cartoon loop
cartoon loop, a//
cartoon rectangular
cartoon rect, a//
cartoon oval
cartoon oval, a//
cartoon tubular
cartoon tube, a//
cartoon arrow
cartoon arrow, a//
cartoon dumbell
cartoon dumbell, a//
b-factor sausage
cartoon putty, a//

ray
ray 2000,2000
ray 5000,5000
viewport 640,480
set ray shadow,0
set ray trace fog,0
set depth cue,0
set antialias,1
png image.png

Hydrogen Bonding
Draw bonds between atoms and label the residues that are
involved.
draw a line between atoms
distance 542/oe1,538/ne
set the line dash gap
set dash gap,0.09
set the line dash width
set dash width,3.0
set the line dash radius
set dash radius,0.0
set the line dash length
set dash length,0.15
set round dash ends
set dash round ends,on
hide a label
hide labels, dist01
label a reside
label (542/oe1), "%s" %("E542")
set label font
set label font id,4
set label colour
set label color,white

Electrostatics
There are a number of ways to apply electrostatics in Pymol. The user can use GRASP to generate a map and then
import it. Alternatively the user can use the APBS Pymol
plugin. Pymol also has a built in function that is quick
and dirty.
generate electrostatic surface action > generate>vacuum
electrostatics > protein contact potential

Pymol Movies (mac)

move the camera
move x,10
turn the camera
turn x,90
play the movie
mplay
stop the movie
mstop
writeout png files
mpng prefix [, first [, last]]
show a particular frame
frame number
move forward on frame
forward
move back one frame
backwards
go to the start of the movie
rewind
go to the middle of the movie
middle
go to the movie end
ending
determine the current frame
get frame
clear the movie cache
mclear
execute a command in a frame mdo 1, turn x,5; turn
y,5;
dump current movie commands
mdump
reset the number of frames per second
meter reset

Miscellaneous

Secondary Structures

NMR Structures

add hydrogens in to a molecule selection

h add
alias a set of commands separated by ; alias go,load
1hpv.pdb; zoom 200/; show sticks, 200/ around 8
structurally align
align prot1////CA, prot2,
object=alignment
fit one molelcule to another
fit selection, target
copy at selection
copy target, source
create a new selection
create target, selection
delete a selection
delete selection
save file
save filename, selection
protect or deprotect a selection [de]protect selection
mask or demask to allow/stop selection
[un]mask
selection
align coordinates with axis
orient selection
get the current rotation matrix
get view
input a rotation matrix
set view
safely refresh the scene
refresh
store a scene
view name, store, description
restore a view
view name, [recall]
set a new colour
set color name, rgb

Pymol has a secondary structure determination algorithm

called dss, however it is better to use the DSSP algorithm
and then define the limits manually.

NMR models should be loaded into the same object, but

should have different states. load a model into an object
load file.pdb, object
show all models in an object
set all states,1
show only one object model
set all states,0
show a particular model
frame model number
determine which model
get model
fit two structures to one another
fit selection
fit and calculate the rms
rms selection
rms without fitting
rms cur selection
fit ensemble structures
intra fit selection,1
calculate rms
intra rms selection,state
ensemble rms without fitting
intra rms cur
selection,state

to run dss
dss selection
to define helical structure
alter 11-40/, ss=H
to define loop regions
alter 40-50/, ss=L
to define strand structure
alter 50-60/, ss=S
rebuild the cartoon after alteration
rebuild
get dihedral angle
get dihedral 4/n,4/c,4/ca,4/cb

Files
change the working directory
list contents of current directory
print current working directory

cd <path>
ls
pwd

Changing Structures

Crystal Structures
of
To recreate crystal packing of molelcules within 5 A
pept in the pept.pdb (which must contain CRYST date),
use the symexp command.
symexp
sym,pept,(pept),5.0

add a bond
remove bonds
join to molecules together

bond atom1, atom2

unbond atom1,atom2
fuse [atom1, atom2]

Old School Images

Load a .pdb and make a cartoon view. Then change the
background colour to white and change the ray mode to 2.
set ray trace mode,2
make the lines thinner
set antialias,2
raytrace the image
ray

c
2007-2009
R. Bryn Fenwick licensed under the terms of the GNU General Public License 2.0 or later.