Hi Amit, You can check between any residues you want. With FindHBond, you can select one set of atoms and then choose the option "Only find H-bonds" with at least one end, exactly one end, or both ends selected, or between the selection and a second set of specified atoms. See the manual: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond... With Find Clashes/Contacts, you can select one set of atoms, "designate" it, then look for contacts among those atoms, or between those atoms and all other atoms, or between those atoms and a second set of designated atoms. See the manual: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash... Both those tools are in the menu under Tools... Structure Analysis. The commands findhbond and findclash have the same capabilities. Here is information on how to "select" atoms in Chimera: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html ...and how to specify atoms in the command line: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html For example, the following command would select residues 12 and 14-16 in chain A of model 0: select #0:12.a,14-16.a I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 31, 2012, at 11:13 PM, Amit Jaiswal wrote:
Dear Elaine, I am stuck with a new problem and that is can I select multiple residues from different chains and check their interaction. There are some results from Haddock and I want to study the interaction residues from different chains. Is it also possible to know their bonding pattern? Please help me out.