Stanley,
PyMOL does have an internal algorithm for identifying and displaying
putative "polar interactions", but unfortunately, it does not current output
such information in a tabulated form as would be necessary / suitable for
any sort of systematic analysis.
dist name, selection1, selection2, mode=2
eg.:
dist pol_conts, chain A, chain B, mode=2
Cheers,
Warren
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From: pymol-users-bounces@...
[mailto:pymol-users-bounces@...] On Behalf Of wayj86
wayj86
Sent: Sunday, August 10, 2008 8:17 PM
To: pymol-users@...
Subject: [PyMOL] Can pymol indentify H-bonds and electrovalent bonds andshow
them?
Hi all,
I am a doctoral candidate of bioinformatics and working on protein-protein
interaction.At present I come across with a problem that given a
protein-protein complex(from PDB or molecular docking),I need a software to
indentify their interactions,which means this program could find out the
atom pairs that forms H-bonds each other,and the residues pairs forming
electrovalent bond by its internal algorism,after the input of the PDB
file.Still I hope these interations can be showed visually.I tried VMD but
it couldn't finish that.So I turn to pymol for help.Could pymol satisfy my
requirement? Thanks a lot for any help.
Best wishes,
Stanley
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