Hi Elaine, First of all thanks for all the suggestions. I would like to know whether the given value of -0.4 for overlap and 0.0 for hbond are optimal enough for finding non-bonded contacts between the protein and ligand. Thanks! Sam Sent from my iPhone
On 22-Jan-2015, at 02:12, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Sam, There is a “findclash” command for finding favorable contacts and close contacts. It has the same features as in the “F ind Clashes/Contacts” graphical interface, so there are many possibilities of different command-line options and the exact command will depend on the settings you want to use: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
I recommend looking at that page to see the full syntax and the command-line options. You could also first try using the graphical interface (menu: Tools… Structure Analysis… Find Clashes/Contacts) to decide what settings you want to use. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
However, here is one example command using some standard settings for finding contacts, assuming that “protein” and “ligand” specify the desired parts of your structure:
findclash protein test ligand overlap -0.4 hbond 0.0 reveal true
… or if your protein was model #0 and your ligand was model #1:17 and you also want to select the contacting atoms:
findclash #0 test #1:17 overlap -0.4 hbond 0.0 reveal true select true
There are many ways to specify atoms (e.g. protein and ligand) in the command line: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
There is another example of using the “findclash” command in the Opened Interface image tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tut orials/squalene.html>
… and the “Find Clashes/Contacts” too is used in the Structure Analysis & Comparison tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
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 Jan 21, 2015, at 2:09 AM, Sam Paul D. <reachsampaul@gmail.com> wrote:
Hi, I need to find non-bonded interactions between a protein and a ligand through command line. Could anyone please suggest which chimera command to use with the syntax? With regards, Sam