[Chimera-users] scan and minimization of dihedral angle

Tue Aug 26 09:47:05 PDT 2014

Eric,
  I've got most things running that I want for my potential energy scan
however  there are a couple of things I still have to do manually. I am
looking for commands or a python script to:

1). clear the "reply log" and then save the results from the "reply log" to
a file
2). create a torsion angle and write that value to a file (Tools->
Structure Analysis -> Angles/Torsions -> select ->create->save)

My current script goes as:

from chimera import runCommand as rc
rc("minimize nogui true")
rc("rotation 1 @C4 at C5")
rc("rotation 1 30")
rc("~rotation 1")
rc("select @C3 at C4@C5 at C6")
rc("minimize nogui true freeze selected")
rc("~select")

rc("rotation 1 @C4 at C5")
rc("rotation 1 30")
rc("~rotation 1")
rc("select @C3 at C4@C5 at C6")
rc("minimize nogui true freeze selected")
rc("~select")

rc("rotation 1 @C4 at C5")
rc("rotation 1 30")
rc("~rotation 1")
rc("select @C3 at C4@C5 at C6")
rc("minimize nogui true freeze selected")
rc("~select")
.
.
.
And so on through a full rotation.

Thanks,

On Mon, Aug 25, 2014 at 7:36 PM, Milo Westler <milo at nmrfam.wisc.edu> wrote:

> 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
> =======================================================================
> ========
>

-- 
-- 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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