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
======================================================================= ========