pyMol cookbook and quick notes by Matteo Paolieri for Protein Crystallography course at the University of Cologne, MS Chemistry, January 2021.
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- License
- Misc
- Distances
- Coloring
- Movies and scenes
- Rendering
- Useful selections
- Protein stability
- Example
- Resources
@path/to/file load the script (plain text)
reinit clear and delete everything
fetch 6ane, async=0 download the pdb and wait
fetch 1w2i, type=2fofc, async=0 download the 2fofc electron density map
get_symmetry object-name-or-selection gives you a tuple of 7 elements: (a,b,c), (α,β,γ) and space group name as e.g. "P212121"
Supercell can display multiple copies of the unit cell.
isomesh mesh1, 1w2i_2fofc, 1.0, active_site, carve=1.6 show electron density map.
mesh is just a name you give.
isomesh var_name, ED_data, map_scale, what-residue-put-here, carving carve cuts out the stuff not related to your active site
set surface_color, gray70
set seq_view, 1 to turn the sequence viewer on.
remove solvent remove solvent (water molecules)
remove Foo remove one selection
copy target, source copy one selection
hide everything, (chain B) hide chain B.
hide all
extract Foo, chain A+B+E+F+G extract the selected chains and call the group Foo
Select every beta sheet beside B and A.
select Asp385, resi 385
show sticks , Asp385
show sticks, br. Foo show Foo as sticks (br is by residue).
Select Asp385 and show it as sticks.
One way to measure distances: Wizard->measure distance
Also, you can click on an object, and get e.g. #/1w2i/C/A/FMT`1092/C, so you can say "measure the distance from the residue 2". mode=2 is the polar mode.
dist polar1, resi 1092, resi 20, mode=2
Select a chain, color it as cyan and then show it as sticks.
select sheetC, (not sheetB) and (not sheetA) and ss s
color purple, sheetC
util.cbc(selection='(all)',first_color=7,quiet=1,legacy=0,_self=cmd) color all by chains, to see what chains you have
color white, all color everything white
color grey70 is a good color
color grey, ss h #h color all alpha helix
color purple, ss s #s color all beta sheets
select cpE, chain E
color cyan, cpE
show sticks, cpE
You can also click on an obect, see its code and color only it by using that specific path.
color gray70, all
color blue, /ca/A/A/TRP`158 # color blue just the W158 in chain A
# Set a scene (maybe after a "set_view"...)
scene electron_density, store
set scene_buttons, 1
# Movie
# It creates a movie from the selected scenes
mset 1x1000 # 30 fps x 33 seconds
mview store, 1, scene=main
mview store, 250, scene=behind
mview store, 450, scene=top
mview store, 750, scene=active_site1
mview store, 900, scene=active_site2
To export a movie: File > Export Movie As...
ray 1920,1080 renders current view in FullHD
# Select Asp385 and color atoms accordingly
select Asp385, resi 385
show sticks , Asp385
select aspzoom, Asp385 expand 5 # select stuff around Asp385
color red, aspzoom and name o* # color all oxygens red
color blue, aspzoom and name n* # color all nitrogens blue
color white, aspzoom and name c* # color the backbone white
center aspzoom
zoom center, 25
Main things to check for protein stability:
- Hydrophobic core (show as spheres; apolar AA)
- Salt bridges
- Disulfide bridges
In general:
Salt bridge (ionic bond):
- AA Acids: Asp+Glu
- AA Basics: Arg+Lys
select basic, resn arg+lys
select acid, resn asp+glu
show sticks, basic
show sticks, acid
color red, basic and name o*
color blue, basic and name n*
color pink, basic and name c*
color red, acid and name o*
color blue, acid and name n*
color pink, acid and name c*
dist name, basic, acid, mode=2
π-π interaction (weak)
select aromatics, (resn phe+tyr+trp+his)
show sticks, aromatics
color pink, aromatics
Solvent interaction
show spheres, solvent # or sticks, etc...
Disulfide bonds
# We have R-S-S-R'. Cys can make them.
select disulfur, resn cys
show sticks, disulfur
color yellow, disulfur
Dipole interactions
It is an interaction between aromatics (Trp, Tyr, Phe) and (Arg, Lys)
select aromatics, resn tyr+trp+phe
select arglys, resn arg+lys
color pink, aromatics
show sticks, aromatics
show sticks, arglys
color red, arglys and name o*
color blue, arglys and name n*
color pink, arglys and name c*
color red, aromatics and name o*
color blue, aromatics and name n*
color pink, aromatics and name c*
dist name, arglys, aromatics, mode=2
Hydrophobics
# Tom Stout, 08/05/2004
# https://pymolwiki.org/index.php/Show_hydrophobics
show cartoon, all
color gray, all
select hydrophobes,(resn ala+gly+val+ile+leu+phe+met)
show sticks, (hydrophobes and (!name c+n+o))
color orange,hydrophobes
disable hydrophobes
set cartoon_smooth_loops,0
Here you can find an example (PETase enzyme) that summarize many useful commands reported here. Just import in pyMol (@path/to/script.pml) and see it.