Dear Dmitry, There is a “findclash” command that has the same capabilities as the “Find Clashes/Contacts” tool. Depending on the cutoffs, you can find just clashes (bad, too-close contacts) or also include longer-range favorable contacts. You could just use the command, or use the GUI to first figure out what settings you want to use with the command. GUI: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html> command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> I recommend the links above for seeing all the options and recommended values, but below are a couple of command examples. To find clashes between molecule models #1 and #3, show as red lines, and write results to Reply Log: findclash #1 test #3 pbColor red log true …and to find contacts between chains A and B of model #0: findclash #0:.A test #0:.B overlap -0.5 hb 0 log true 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 Aug 25, 2015, at 5:10 AM, Dmitry <semchonok@gmail.com> wrote:

Dear Colleagues, I have 3d tetramer volume density where I fitted known x-ray structure of monomer (to each unit of tetramer). I want to check the inter-monomeric space, whether there is connections between 2 monomers. Is there a command or script that checks the presence of contacts between bounds of 2 structures? Thank you Sincerely, Dmitry