Hi Hani, with PyMOL you can visualize polar contacts, using the "distance" command with "mode=2" argument. See the PyMOLWiki page: http://pymolwiki.org/index.php/Distance
Example: distance interface, chain A, chain B, mode=2 However, this is not really a analysis of the interface. Instead I would suggest to use the PISA webserver: http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Hope that helps. Cheers, Thomas syed.abidi wrote, On 03/19/12 12:19: > Dear All, > > I have a small query regarding PyMol and I would appreciate if you > can help me with it. My query is: > > How do I analyze interactions with PyMol after I have docked my > files? I wanted to know which molecules/amino acids are interacting in the > docked confirmation. > I would really appreciate your help. > > Thanks, > > Hani -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
