here it is:
http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts

vitali

On Mon, Nov 21, 2011 at 8:50 AM, rjayashree13-science@yahoo.co.in <rjayashree13-science@yahoo.co.in> wrote:
Thank you. It works, but it does not bring out the type of interaction responsible for interface contact-hydrogen bonding or electrostatic interaction etc.
 I am using another tool called PSAP for analyzing inter-molecular interactions (iris.physics.iisc.ernet.in/psap)
It gives me the residues involved in hydrogen bonding, now using Pymol I can label these residues, but is there any way to depict these hydrogen bonds also and the distances?
 
Dr. Jayashree Ramana



From: Vitali Stanevich <stanevich@wisc.edu>
To: "rjayashree13-science@yahoo.co.in" <rjayashree13-science@yahoo.co.in>
Cc: "pymol-users@lists.sourceforge.net" <pymol-users@lists.sourceforge.net>
Sent: Sunday, 20 November 2011 1:57 PM
Subject: Re: [PyMOL] query

check this out:
http://www.pymolwiki.org/index.php/InterfaceResidues

if you want faster and easier, but less reliable (in my opinion) way, you can analyze your .pdb with PISA:
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html

vitali

On Sun, Nov 20, 2011 at 1:51 AM, rjayashree13-science@yahoo.co.in <rjayashree13-science@yahoo.co.in> wrote:
I have a PDB file for a dimeric protein. Is it possible to depict the intersubunit contacts for any PDB file? Is Pymol alone sufficient for this purpose or will it only help visualization?
Could you also tell me which commands in Pymol can I use for this purpose? I have tried a lot but could not get an answer to this. I will be very thankful for the favour.
 
Dr. Jayashree Ramana

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