Hi Anasuya,
This sound like one of those very good reasons to have a go at Python,
and leave Perl behind... Together with all the plain reasons to leave
Perl behind :) First of all, check http://xkcd.com/353/
Assuming the file is called list.txt and you have all pdb files at
hand (which is not strictly necessary, as PyMOl can download them for
you), make a file called process.py with the following content
from pymol import cmd
def process_line(x):
pdbid,res,chain,num = x.split()
cmd.load(pdbid+".pdb")
cmd.select("zone1","byres all within 4.5 of (chain %s and resn %s
and resi %s)"%(chain,res,num))
cmd.select("zone2","(byres all within 4.5 of zone1) and not zone1)")
cmd.save("%s-%s-%s-%s-zone1.pdb"%(pdbid,res,chain,num),zone1)
cmd.save("%s-%s-%s-%s-zone2.pdb"%(pdbid,res,chain,num),zone2)
cmd.delete(pdbid)
def process_all(filename):
for line in open(filename):
process_line(line)
process_all("list.txt")
#======
After saving the file, do
pymol -c process.py
And that's it. Unless I made an error somewhere :P I haven't actually
tested this. But the proper solution should lie along these lines :)
Hope it helps,
Tsjerk
On Thu, Sep 29, 2011 at 8:58 AM, Anasuya Dighe
<anas...@mbu.iisc.ernet.in> wrote:
> Hello,
> I have a .txt file which has data in the following fashion:
>
> 19gs BSP A 1
> 1a2d PYX A 117
> 9rsa ADU A 125
> 7kme PRR J 382
> 1a0r ACE B 1
> 1a0r FAR G 72
> .
> .
> .
>
> Fields: <PDB ID> <LIGAND NAME> <CHAIN TO WHICH IT IS ATTACHED> <RESIDUE
> SEQUENCE NUMBER>
>
> In such a way, I have data of around 19,200 unique pdb files which have one
> or
> more ligands attached to them. [PLEASE NOTE THAT there can be multiple ligands
> to a particular .pdb file attached at different positions ]
>
> For each .pdb file, I need to extract complete residues which fall within a
> radius of 4.5 Angstroms of the ligand. I am calling such zones as ZONE1.I mean
> residues that have any atom within 4.5 Angstroms of the ligand => zone1
> Then after extracting ZONE1, I also want to extract complete residues which
> fall
> within a radius of 4.5 Angstroms of ZONE1.. I am calling these zones as
> ZONE2. I
> mean, residues that have any atom within 9.0 Angstroms of the ligand, but are
> not already in ZONE1 => ZONE2
>
> I am looking for a way to automate Pymol by writing a .pml script, such that
> foreach pdb file, I have 2 additional files generated such that they are
> called
> as: 19gs_BSP_z1.pdb [for ZONE1] and 19gs_BSP_z2.pdb [for ZONE2],
> 1a2d_PYX_z1.pdb, 1a2d_PYX_z2.pdb and so on...
>
> Can this be done through PERL?
> Please suggest me an efficient way of achieving the desired output..
>
> Thanks,
>
> -Anasuya
>
>
>
> --
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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
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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