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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