Pymol Cheatsheet

- General
bg white                       # Turn background color to white
save rna6.pse                  # Save your working session to pse file
set valence, 1                 # Show double bonds.
h_add                          # Show hydrogens.  
pymol -qc bla.pml >& bla.log & # To invoke without X11 display
pymol -M                       # Invoke mono mode instead of stereo. Avoid flicker.
unbond (id 8), (id 2)          # To remove a bond between atoms
bond (id 8), (id 2)            # To create a bond between atoms
select carbons, symbol c       # Select all carbon atoms and call them carbons.
color black, carbons           # Color the carbons selection black.
disable selectionname          # Hides/disables a loaded structure(selection).
enable selectionname           # Shows/enables a loaded structure(selection).
set internal_gui, 0            # Hide object control panel
- Labels
label (n;C1'), "%s" % (name)
set label_color, black
set label_font_id, 4	
set label_size, 3
set label_position, [2,0,0]
show labels
- Spheres
set sphere_scale, 0.25
- Sticks
show sticks, selectionname
set stick_radius, 0.1
set stick_ball, on #Makes the stick command show ball and stick
set stick_ball_ratio, 1.5
- Ribbons
set ribbon_color, marine
set ribbon_width, 2
set ribbon_sampling, 1
set ribbon_smooth, 1
- Cartoon
cartoon putty
set cartoon_ladder_mode, 0
set cartoon_transparency, 0.5
set cartoon_ring_finder, 0
cartoon dumbbell
set cartoon_dumbbell_width, 0.2
set cartoon_dumbbell_radius, 0.4
set cartoon_color, marine, resi 34-67
set cartoon_color, blue, resi 68,78
show cartoon
- Ray tracing
set ray_trace_mode, 3
set ray_trace_fog,0
set ray_shadows,0
set depth_cue, 0              #This one with care or it might look funky.
set antialias,1
set ray_trace_gain, 0.005
png img1.png, width=1600, height=1200, dpi=600, ray=1
- Rotating ("turn" to rotate all loaded objects, "rotate" for individual objects)
turn x, 10
- Surfaces
set transparency, 0.65, i. 1-100
set cgo_transparency, 0.4
- Aligning Structures (They must have the same number of atoms and be the same molecule)
pair_fit rna2////C5, rna1////C5, rna2////C4, rna1////C4
pair_fit (rna2 and id 12+56), (rna1 and id 12+56)
- Displaying all states in a multi-state pdb, say, an NMR file and coloring by B-factor.
set all_states, on
spectrum b, yellow_white_red, minimum=48, maximum=100
spectrum b, rainbow2_rev
- Loading multiple pdb files into a multistate object (allfiles) using the python glob module

import glob
for x in glob.glob("Folder/*.pdb"): cmd.load(x, "allfiles")
- Draw a trace cartoon (or ribbon) based on atoms different than P or Calpha.
set cartoon_trace_atoms      #Note that ribbon_trace_atoms also works
cartoon tube
show cartoon, selection and name C1'
- Counting atoms
select catoms, name c*
print cmd.count_atoms("catoms")
- Showing a slider after loading a trajectory
set movie_panel=1
set movie_panel_row_height, 20

- Scripts.
run ~/bin/
Invoking the previous scripts will color and select nucleic acid bases.
Scripts are found at

- As a one liner.
Pymol can also be invoked as a one liner to use its modules. For example, say you want to load your pdb and save it in FASTA format.
pymol -qc -k  -d "load bigoleprotein.pdb; save bigoleprotein.fasta"
And it never pops-up the rendering window!. For more info on command line options in pymol you can search for that page in the pymol wiki.

- Link to full set of pymol settings.

- Michael Sykes webpage with very useful pymol tips and tricks

- Movie making in pymol.

- Gif movies.

- Modified coloring by base script.

- Selection keywords.

- Command line options.

- PyMOL User's Guide.

- Repository of Simple Molecules.

- Molecular Sculpting

- Example 1 -