Re: [PyMOL] Putting a protein molecule into a grid and traversing through the grid

[Tsjerk W. <ts...@gm...>]

Hey :)

Does the script pasted below do what you want? It does not move the
molecule(s), but it returns a list of occupied bins with the ids,
names and chains of residues in it.

Hope it helps,

Tsjerk

###

from pymol import cmd

def _bin(x,d):
    d = float(d)
    a,b,n = min(x),(1-1e-16)/(max(x)-min(x)),int((max(x)-min(x))/d+0.5)
    return [ int(b*(i-a)*n)*d for i in x ]

def bin(sele="all",d=5):
    m = cmd.get_model(sele)
    b = zip(*[ _bin(i,5) for i in zip(*m.get_coord_list()) ])
    print b
    d = dict()
    for i,j in zip(b,m.atom):
        d[i] = d.get(i,[]) + [(j.resi, j.resn, j.chain)]
    return d.items()




On Thu, Oct 27, 2011 at 4:25 PM, Thomas Holder
<sp...@us...> wrote:
> Hi Anasuya,
>
>> how do i put a protein molecule inside a cube with x-axis spanning till the
>> largest x-coordinate, y-axis spanning till the largest y-coordinate, and z-axis
>> spanning till the largest z-coordinate?
>>
>> Once i do this, can i divide the larger cube(i.e. the one holding the entire
>> protein) into smaller ones of lesser dimensions? Say, 5A x 5A x 5A?
>
> I'm not aware of any straightforward solution for this. You could write
> a python script that creates selections for each (sub)cube, but I guess
> it will be a quite complex script. Have a look at
> http://pymolwiki.org/index.php/SelInside which should cover all
> necessary API functions.
>
>> Once i generate these smaller cubes, is there a way via pymol, by which i can
>> navigate through the protein molecule, (smaller)cube by (smaller)cube?
>> As in, can pymol be used to tell me which residues are lying in which (smaller)
>> cube and so on?
>
> If you have selections for each cube, try this to lookup cubes that
> contain atoms of residue number 10:
>
> print cmd.get_names('public_selections', 0, 'resi 10')
>
>> Can all this be done in a single pymol window/script?
>> please let me know.
>>
>> Thanks
>> -Anasuya
>
> Cheers,
>   Thomas
>
> --
> Thomas Holder
> MPI for Developmental Biology
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands