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2014-03-28T02:00:42Z

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Newacct at 08:13, 27 November 2009

2009-11-27T08:13:34Z

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== Overview ==
This script filters through all the PDBs in the parent dir (you can easily the the directory it scans). For each molecule, it saves '''just''' the ligands/heteroatoms (excluding the waters). This gives you a simple way to filter through a database of proteins looking only at their ligands.

This script, as noted below, works on the objects at the level of a '''molecule'''. While we can [[iterate]] over atom number (ID), residue number (resi), etc we do not have any such "MOLID". So, we provide this simple workaround. You might need this file because if you have a residue (like #111 from 3BEP) that consists of a molecule and an atom then there's no other way to save the separate pieces (of molecule/atom) into two (or more files). As you can see in the following listing, if we iterate over the hetero atoms (and not waters) in 3BEP we get,
<source lang="python">
PyMOL>iterate bymol het, print resi, resn, ID, chain, segi, alt
111 5CY 6473 C
111 5CY 6474 C
111 5CY 6476 C
111 5CY 6477 C
111 5CY 6478 C
111 5CY 6479 C
111 5CY 6480 C
111 5CY 6481 C
111 5CY 6482 C
111 5CY 6483 C
111 5CY 6484 C
111 5CY 6485 C
111 5CY 6486 C
111 5CY 6487 C
111 5CY 6488 C
111 5CY 6489 C
111 5CY 6490 C
</source>
which does not allow us to separate the two pieces.

== The Code ==
<source lang="python">
python

#
# This simple script will filter through all PDBs in a directory, and for each one
# save all the ligands/heterotoms (that aren't waters) to their own file. This
# script operates at the level of molecules, not residues, atoms, etc. Thus, if
# you have a ligand that PyMOL is treating as ONE residue, but is actually two
# separate molecules, or a molecule and an atom, then you will get multiple files.
#

from glob import glob
from os import path
from pymol import stored

theFiles = glob("../*.pdb");

for f in theFiles:
# load the file
cmd.load(f);
# remove the protein and waters
cmd.remove("polymer or resn HOH");

cmd.select("input", "all")
cmd.select("processed", "none")
mol_cnt = 0

while cmd.count_atoms("input"):
# filter through the selections, updating the lists
cmd.select("current","bymolecule first input")
cmd.select("processed","processed or current")
cmd.select("input","input and not current")

# prepare the output parameters
curOut = path.basename(f).split(".")[0] + "_" + str(mol_cnt).zfill(5) + "_het.pdb"
curSel = "current"

# save the file
cmd.save( curOut, curSel );
print "Saved " + curSel + " to " + curOut

mol_cnt = mol_cnt + 1;

# remove all to move to next molecule
cmd.delete("*");

python end
</source>

[[Category:Script_Library]]
[[Category:System_Scripts]]

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Pyadmin: 3 revisions

Newacct at 08:13, 27 November 2009