Re: [PyMOL] Creating dummy zones

[Jason V. <jas...@sc...>]

Hi Anasuya,

As you choose your zones just check for overlaps in selections. It
might look something like this:

# good zones

good_zones = set()

# some sampler you choose, just returns an array of atom selections

zones = get_zones()

for x in range(len(zones)):
    for y in range(x+1,len(zones)):
        if cmd.count_atoms("%s and %s" % y, x) != 0:
            print "Msg: Ignoring zone %s as it overlaps with zone %s" % (y,z)
        else:
            good_zones.add(y)

print "Good zones for this protein: "
print good_zones

Cheers,

-- Jason

P.S. I bet Tsjerk has a few cool ideas on this.



On Tue, May 1, 2012 at 4:29 AM, Anasuya Dighe <an...@mb...> wrote:
> Hi,
> I have around 18000 ligand-bound PDB's. I have as of now, extracted zones of
> amino acid residues (say ZONE-1) which are within a radius of 4.5A from the
> ligand, for each of the (18000) ligand-bound PDBs with me.
> How do I now go about generating, similar RANDOM zones of amino acid residues
> occurring over a radius 4.5A, across the protein structure, such that they don't
> overlap with each other and ALSO the original ZONE-1 corresponding to that
> PDBID?
> Lets say, for each of the 18000 PDBIDs that I have, I want to create 5 such
> distinct 'dummy' zones of radius 4.5A, with the condition that they dont overlap
> with each other and also with my earlier ZONE1.
>
> In simpler terms:
> (Original PDB ID)1abc.pdb,
> (Zone1 corresponding to 1abc.pdb) 1abc_ZONE1.pdb,
> (Five dummy zone1's extracted for the same pdb such that they are not
> overlapping with my earlier Zone1 AND WITH EACH OTHER) 1abc_z1_dummy1.pdb,
> 1abc_z1_dummy2.pdb, 1abc_z1_dummy3.pdb, 1abc_z1_dummy4.pdb, 1abc_z1_dummy5.pdb
>
> How do I modify this existing python script, so that I can generate these dummy
> zone1 pdb's?
> { Given I have file_1.txt containing a list of PDBid's, LIgand name, its chain
> ID and resi number. }
>
> from pymol import cmd
> def process_line(x):
>  pdbid,res,chain,num = x.split()
>  cmd.load(pdbid)
>  cmd.select("zone1","byres all within 4.5 of (chain %s and resn %s and resi %s
> and not resn HOH)"%(chain,res,num))
>  cmd.save("%s-%s-%s-%s-zone1.pdb"%(pdbid,res,chain,num),"zone1")
>  cmd.delete(pdbid)
>
> def process_all(filename):
>  for line in open(filename):
>   process_line(line)
>
> process_all("file_1.txt")
>
> Thanks.
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120