View and Themes
background color
Display Amino Acid
set seq_view, onset seq_view_format, 0
Add something
Add Hydrogen bonds
Add Hydrogen bonds: PyMOL tutorial
Action → find → polar contacts → select from menu
Remove something
cite: © Jan-Philip Gehrcke; 2011
remove (hydro) remove hydrogens remove resn hoh remove solvent
cmd.get_chains: ['A', 'B', 'C', 'H', 'L']
PyMOL>replace C,4,4
Amino Acid Sequence
source: pymolwiki
print (cmd.get_fastastr('all' ))print (cmd.get_fastastr('5WL2 and chain B' ))
>5WL2_H
QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQGRVTI
TADESTSTAYMELSSLRSEDTAVYYCARHGNYYYYSGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTS
GGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKP
SNTKVDKRVEPKSCHHHHHH
>5WL2_L
QSVLTQPPSVSEAPRQRVTISCSGSSSNIGNNAVNWYQQLPGKAPKLLIYYDDLLPSGVSDRFSGSKSGT
SASLAISGLQSEDEADYYCAAWDDSLNGAVFGGGTQLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLI
SDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTV
APTECS
...
Object manipulation
movement
rotate y,-.2, 4fqh rotate x,-.2, 4fqh rotate z,-.2, 4fqh
hide chain
hide representation [,object] hide representation [,(selection)] hide (selection)
Show Chain
show cartoon, Mos99 and chain A chain B
Colors for Pymol
pymolwiki: Colors’ name and values
Assign the name of color into an object
color red, Mos99 select part1, Mos99 and chain A and resi 50+56+60 color hotpink, part1
Example of set a color by RGB value and assign it into an object
set_color red2, [1,0.3,0.01] color red2, Mos99
Strcture align
fetch 1oky 1t46, async=0 align 1oky, 1t46 align 1oky, 1t46, object=alnobj save alignment.aln, alnobj align 1oky, 1t46, cycles=0, transform=0
Partial structure align
Cite: Queen’s University
align 5cha and resi 1-100, 2xxl and resi 300-400 align structure2 & i. 1-100, structure 1 & i. 300-400 align structure2 and resi 1-100 and name n+ca+c+o, structure1 and resi 300-400 and name n+ca+c+o align structure2 & i. 1-100 & n. n+ca+c+o, structure1 & i. 300-400 & n. n+ca+c+o
Align chains
align 5cha and chain A+B+C, 2xxl and chain A
Atom
Atom color
color grey90, 2xxl color grey80, 2xxl 5cha
Select Atom
Select Properties
PyMol select aas, resn ASP+GLU in 2xxl
Create a variate ass which contain all ASP and GLU residues.