Thanks. I tried using the easy method and it didn't work. Here is my script: from chimera import runCommand as rc rc("minimize") rc("~select") rc("rotation 1 @C2@C3") rc("rotation 1 90 1") rc("select :@C1@C2@C3@C5") rc("minimize freeze selected") If I did the first command in a script, followed by a separate script using the next 3 commands, then another separate script for the last 2, it worked. If I have done something wrong, please tell me. Obviously, I could write a bunch of scripts and run them separately, but I was trying to be efficient. I want to do a potential energy scan with smaller angles (~10 degrees or so). I can write a script to write all of these separate scripts and then run them in tandem, but that can be rather tiring. I am also interested in using chimera python scripts ( I promised myself I would learn python). I also sent a second message asking how to write out the parameters determined from antechamber. (write prmtop doesn't work for me) On Sun, Aug 24, 2014 at 1:32 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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 ======================================================================= ========
-- -- 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 ======================================================================= ========