Re: [chimera-dev] Automate Energy Minimization of pdb files

Hi Ajay, My advice is to first figure out exactly which Chimera commands you want to use for each structure. You would do that by entering the commands manually in the Command Line (show Command Line using Favorites menu) to try them. The relevant commands are “open" “addh” “addcharge” “minimize” and “write” which all have various options: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html Then, after you have figured out the desired commands/options, see this page for how to use script looping through multiple structures. http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.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 20, 2017, at 3:53 AM, Ajay Pal wrote:

Dear Developers I am trying to build a chimera integrated python script to energy minimize protein pdb files.

I have a list of ~400 pdb files (clean homology models) which I need to Energy minimize Can you please help me with this matter: like how to select files from directory adding H-atoms selecting the forcefield, etc how can I automate this whole process ?

Thank you, I would appreciate all your help. Ajay