Hi Devan, Often people will use the Chimera commands in combination with python or shell scripts to do that sort of thing. The FindHBond tool is also implemented as the "findhbond" (or "hbonds" command). First you would figure out the command equivalent of the options you use in the dialog, usually by trying things in the Command Line. You can show the Command Line from the Favorites menu. Enter command "help findhbond" to see the findhbond manual page.

Then, for looping through multiple proteins, see here: http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html

If you haven't use commands much you may want to try the "getting started with commands" tutorial first. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.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 Jul 24, 2013, at 11:02 AM, Devan Bicher thedevanbicher@gmail.com wrote:

To Whom it may concern, Hi, my name is Devan Bicher and I am a researcher at Lehigh University. I am working on computational studies of proteins and Chimera's findHBond function is extremely useful! I have been using chimera a lot recently, however since I am working with a number of different protein/substrate combinations it would be great for me to use findHbond in a batch sort of way in which I can supply numerous inputs and allow chimera to run on all of them. Does chimera have any sort of built in batch processing option like this?