[Chimera-users] scan and minimization of dihedral angle

[Milo Westler]

Thanks for your help. Is there a command line to clear the reply log?


On Mon, Aug 25, 2014 at 1:18 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> 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
> <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
>
> --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
>
>
>
>


-- 
-- 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
=======================================================================
========
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