[PyMOL] Creating dummy zones

[Anasuya D. <an...@mb...>]

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.


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