[Chimera-users] scan and minimization of dihedral angle

Eric Pettersen pett at cgl.ucsf.edu
Mon Aug 25 11:18:01 PDT 2014


On the minimize commands you want to add "nogui true", which will cause the minimization to proceed using default settings rather than querying you for hydrogen addition method, charge settings, etc.  Otherwise the command brings up dialogs for those things and then releases control back to Chimera, which causes your script to continue on to the other commands without the minimization having actually occurred yet.

If you want non-default choices for hydrogen addition, etc. you will have to put those commands in front of the minimize command.

You probably also want to check out the simple primer for scripting Chimera, here:  Very Basic Chimera Programming Primer

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Aug 24, 2014, at 2:04 PM, Milo Westler <milo at nmrfam.wisc.edu> wrote:

> 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 at C3")
> rc("rotation 1 90 1")
> rc("select :@C1 at C2@C3 at 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 at 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 at 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 at 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 at nmrfam.wisc.edu
> PHONE: (608)-263-9599
> FAX: (608)-263-1722
> ======================================================================= ========
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


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