Hi All Pymol users
I have a set of 40 X-ray
crystallographic structures complexed with inhibitors belonging to a
specific family of kinases. Binding site residues within 5 angstrom
from the inhibitor were selected for each PDB
Hi Renuka,
With a little bit of Python programming and better understanding of
structure alignment in PyMOL you should be able to complete your task.
First, check out the structure alignment category on the PyMOLWiki (
http://www.pymolwiki.org/index.php/Category:Structure_Alignment). Read the
rms and fit gave you different values? They have never given me different
values.
Example:
from pymol import cmd
cmd.fetch('1nmr')
cmd.split_states('1nmr')
for i in xrange(1,21):
for j in xrange(1,21):
prot_i = '1nmr_%04d' %i
prot_j = '1nmr_%04d' %j
rms_val =
