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 #movie.add_state_sweep(1,0,start=1) movie.add_state_loop(1,0,start=1) set movie_panel_row_height, 20
- Scripts.
run ~/bin/charmmcolors.py @~/bin/colorbybase.pyInvoking the previous scripts will color and select nucleic acid bases.
Scripts are found at http://mesguerra.net/scripts
- 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
- Modified coloring by base script.
- Repository of Simple Molecules.