From: kun y. <yan...@ya...> - 2006-12-08 20:24:09
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Hi,all I want to show all the H-bonds and VDW between two dimer interface. Would you please tell me how I use pymol to do this? Thank you very much. ___________________________________________________________ 雅虎免费邮箱-3.5G容量,20M附件 http://cn.mail.yahoo.com/ |
From: Robert I. <imm...@gm...> - 2006-12-11 15:18:47
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Kun, When I'm interested in dimer interfaces, or protein ligand contacts I usually use Molprobity to define the interface. http://molprobity.biochem.duke.edu/ It is a bit of a process, but here's the rundown: Load your .pdb into molprobity Add hydrogens Visualize interface contacts Then select your two 'half-interfaces' and run probe One of the output from this is a list that has: residue from half 1 : residue from half 2 : contact type : details I usually will take this list of residues and display them in pymol, then add dashes for hydrogen bonds using the dist command -bob |