Hi Milo, You can script most of it with Chimera commands: activate torsion (do that part just once), increment torsion with “rotation”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rotation.html> select atoms to be frozen (or not) in minimization with “select": <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html#newer> “minimize” command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html> That would still entail saving the Reply Log and editing it yourself. For saving log contents, these previous posts may be useful: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003184.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-July/005367.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 Aug 24, 2014, at 8:11 AM, Milo Westler <milo@nmrfam.wisc.edu> wrote:
Hi, I want to to a potential energy scan of a dihedral (of a small organic molecule) by setting a dihedral angle, fixing those atoms involved, and doing a minimization. Then incrementing the angle and repeating. I can currently do all of this by using the gui (set torsion angle in build_structure,minimize with selected atoms fixed , then save and edit the final energies for each angle in reply log). I'm sure that this can be done with python. I am wondering if there is an available script to do this all. As input I would have a set of torsion angles and as output I would like a table of angle and energy.
-- -- Milo =================================================== National Magnetic Resonance Facility at Madison An NIH-Supported Resource Center
W. Milo Westler, Ph.D.
NMRFAM Director Senior Scientist and Adjunct Professor Department of Biochemistry University of Wisconsin-Madison DeLuca Biochemistry Laboratories 433 Babcock Drive Rm B160D Madison, WI USA 53706-1544 EMAIL: milo@nmrfam.wisc.edu PHONE: (608)-263-9599 FAX: (608)-263-1722 ======================================================================= ========