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 -- DeLano Scientific LLC Subscriber Support Services mailto:[email protected]
_____ From: [email protected] [mailto:[email protected]] On Behalf Of wayj86 wayj86 Sent: Sunday, August 10, 2008 8:17 PM To: [email protected] 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 -- Just have a little faith -- Just have a little faith
