[PyMOL] loop through many pdb files and show their centre of masses

[Zakir T. <zak...@gm...>]

Hi there,

I have no experience in scripting what so ever thus this simple task drives me nuts.
I was using ZDOCK to dock my protein on the complex. It spits me out 2000 pdb files that each contain a ligand and receptor. Receptor position is fixed, ligand is not. What I want to show is just centre of mass of the ligand and a receptor. I understand that I should be doing something like this:

from pymol import cmd
from glob import glob
 
for file in glob("*.pdb"):
    print file
    cmd.load(file,'prot')
    for a in cmd.index("CYS/SG"):
        identify COM
print its location as a dot or sphere
delete loaded file 
go to another one until list is exhousted

    cmd.delete("all”)

Thank you a lot and sorry for bothering you with such a silly question!


zak...@gm...