<div dir="ltr"><div>Thanks. I tried using the easy method and it didn't work. Here is my script:<br><br>from chimera import runCommand as rc<br>rc("minimize")<br>rc("~select")<br>rc("rotation 1 @C2@C3")<br>
rc("rotation 1 90 1")<br>rc("select :@C1@C2@C3@C5")<br>rc("minimize freeze selected")<br><br><br><br></div><div>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).<br>
<br>I also sent a second message asking how to write out the parameters determined from antechamber. (write prmtop doesn't work for me)<br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sun, Aug 24, 2014 at 1:32 PM, Elaine Meng <span dir="ltr"><<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Milo,<br>
You can script most of it with Chimera commands:<br>
<br>
activate torsion (do that part just once), increment torsion with “rotation”:<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rotation.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rotation.html</a>><br>
<br>
select atoms to be frozen (or not) in minimization with “select":<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html#newer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html#newer</a>><br>
<br>
“minimize” command:<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html</a>><br>
<br>
That would still entail saving the Reply Log and editing it yourself. For saving log contents, these previous posts may be useful:<br>
<<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003184.html" target="_blank">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003184.html</a>><br>
<<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-July/005367.html" target="_blank">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-July/005367.html</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<div class="HOEnZb"><div class="h5"><br>
On Aug 24, 2014, at 8:11 AM, Milo Westler <<a href="mailto:milo@nmrfam.wisc.edu">milo@nmrfam.wisc.edu</a>> wrote:<br>
<br>
> Hi,<br>
> 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.<br>
><br>
> --<br>
> -- Milo<br>
> ===================================================<br>
> National Magnetic Resonance Facility at Madison<br>
> An NIH-Supported Resource Center<br>
><br>
> W. Milo Westler, Ph.D.<br>
><br>
> NMRFAM Director<br>
> Senior Scientist<br>
> and<br>
> Adjunct Professor<br>
> Department of Biochemistry<br>
> University of Wisconsin-Madison<br>
> DeLuca Biochemistry Laboratories<br>
> 433 Babcock Drive<br>
> Rm B160D<br>
> Madison, WI USA 53706-1544<br>
> EMAIL: <a href="mailto:milo@nmrfam.wisc.edu">milo@nmrfam.wisc.edu</a><br>
> PHONE: <a href="tel:%28608%29-263-9599" value="+16082639599">(608)-263-9599</a><br>
> FAX: <a href="tel:%28608%29-263-1722" value="+16082631722">(608)-263-1722</a><br>
> ======================================================================= ========<br>
<br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br><div dir="ltr">-- Milo<br>===================================================<br>National Magnetic Resonance Facility at Madison<br> An NIH-Supported Resource Center<br>
<br>W. Milo Westler, Ph.D.<br><br>NMRFAM Director<br>Senior Scientist<br> and<br>Adjunct Professor<br>Department of Biochemistry<br>University of Wisconsin-Madison<br>DeLuca Biochemistry Laboratories<br>433 Babcock Drive<br>
Rm B160D<br>Madison, WI USA 53706-1544<br>EMAIL: <a href="mailto:milo@nmrfam.wisc.edu" target="_blank">milo@nmrfam.wisc.edu</a><br>PHONE: (608)-263-9599<br>FAX: (608)-263-1722<br>======================================================================= ========</div>
</div>