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

Hi,

AFAIK, pseudoatom puts a new atom on the center of mass (or geometry) of
the selection. So,

import glob
from pymol import cmd

for pdb in glob.glob("*.pdb"): cmd.pseudoatom(pdb[-3:],"{} and resn
LIGANDNAME".format(pdb))

Or along those lines. Be creative :)

Cheers,

Tsjerk


On Tue, Sep 15, 2015 at 12:25 AM, Osvaldo Martin <alo...@gm...>
wrote:

> Hi Zakir,
>
> The following script computes the Center Of Mass (or alternative the
> geometric center) and then draws a pseudoatom
> <." rel="nofollow">http://www.pymolwiki.org/index.php/Pseudoatom>. I think you could adapt
> the script to your needs if you find difficulties, don’t hesitate to
> contact the list again (your question is not silly).
>
>
> import pymol
> from pymol import cmd
> pymol.finish_launching()
> import numpy as np
>
> def center(selection, com=True):
>     model = cmd.get_model(selection)
>     xyz = np.array(model.get_coord_list())
>     mass = [i.get_mass() for i in model.atom]
>     xyz_m = xyz * np.array([mass]).T
>     if com:
>         return tuple(np.sum(xyz_m, 0)/model.get_mass())
>     else:
>         return tuple(np.average(xyz, 0))
>
>
> cmd.load('some_file.pdb')
> COM = center('all')
> cmd.pseudoatom('center', pos=COM)
>
> Alternatively, you can use this script
> <" rel="nofollow">http://www.pymolwiki.org/index.php/Center_of_mass> to compute the center
> of mass.
>
> Cheers,
> Osvaldo
>
>
> On Mon, Sep 14, 2015 at 4:29 PM, Zakir Tnimov <zak...@gm...>
> wrote:
>
> 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...
>>
>>
>>
>>
>>
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>
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-- 
Tsjerk A. Wassenaar, Ph.D.