From: kun yang <yangkunn2000@ya...> - 2006-12-08 20:24:09
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.
From: Robert Immormino <immormino@gm...> - 2006-12-11 15:18:47
When I'm interested in dimer interfaces, or protein ligand contacts I
usually use Molprobity to define the interface.
It is a bit of a process, but here's the rundown:
Load your .pdb into molprobity
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
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