Dear PyMOL List
It comes up once in a while, is it possible to use PyMOL features from
outside of PyMOL? An example, the below is a script (inspired by Thomas
Holder) which saves down to disk all amino acids of a protein structure
into separate PDB files.
# *****************************************************************
from pymol import cmd
from pymol import stored
from pymol.exporting import _resn_to_aa as one_letter
# *****************************************************************
def seq(state, selection="name ca or resn hoh or resn lig"):
print "Generating seqs."
cmd.select("prot", selection)
while cmd.pop("_tmp", "prot"):
cmd.iterate("_tmp", "stored.x=(resn,resv)")
#print stored.x[0], stored.x[1]
# Special case 1: Waters.
if stored.x[0] == 'HOH':
filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
# Special case 2: Substrate.
elif stored.x[0] == 'LIG':
filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
# Other: protein back-bone.
else:
filename = 'seq-%s%d-%s.pdb' % (one_letter[stored.x[0]].lower(),
stored.x[1], state)
cmd.save(filename, "byres _tmp")
cmd.delete('_tmp prot')
cmd.extend('seq', seq)
# -----------------------------------------------------------------
Is it possible to somehow include this in a Python script, and running
it from the command line? If not, why?
Thanks for any feedback.
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