[Chimera-users] swapaa: choosing rotamers

Repic Matej matej.repic at epfl.ch
Thu Jul 9 05:43:46 PDT 2015

Dear Alex,

Instead of calling chimera from a python script, you can simply use chimera's python to run the script and call the command line commands with the runCommand() function. This way, you can have just the python script and avoid the cmd dependency.

You can run the following script with "chimera --nogui script.py":

import chimera
from chimera import runCommand as rc
rc('open 1BPT')
rc('swapaa tyr :5; swapaa phe :7')


Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
BCH 4108
CH - 1015 Lausanne

From: <chimera-users-bounces at cgl.ucsf.edu<mailto:chimera-users-bounces at cgl.ucsf.edu>> on behalf of roz orchidea <roz.orchidea at gmail.com<mailto:roz.orchidea at gmail.com>>
Date: Thursday, July 9, 2015 at 12:49
To: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Re: [Chimera-users] swapaa: choosing rotamers

Thank you both for your answers!
Eric I am not trying all rotamers, I just want to have some specific rotamers in the binding sites of my protein-DNA models. I am using a python script to call chimera and a cmd script with all the swapaa commands that I need. Is there another way?

Thank you for your time,

2015-07-01 19:03 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu<mailto:pett at cgl.ucsf.edu>>:
Also, the "lib" keyword to the swapaa command allows you to pick the library to use, e.g.:  swapaa ASP :41.a lib dynameomics criteria 2


On Jul 1, 2015, at 10:01 AM, Eric Pettersen <pett at cgl.ucsf.EDU<mailto:pett at cgl.ucsf.EDU>> wrote:

> Hi Alex,
>       To get specifically get the second most probable rotamer you add the "criteria" keyword to the swapaa command with the value "2", e.g.:  swapaa ASP :41.a criteria 2
>       You don't really say why you specifically want the second rotamer.  Are you trying out all the rotamers one by one?  You might want to consider doing that via the a Python script that uses the functions in the Rotamers module.  That way you can find out how many rotamers are available, which isn't really possible with just the swapaa command.
>       Another thing to consider is that if you know the chi angles you want, you can just swap to the new residue type and then request those specific chi values.  For example to change residue 41.A to ASP and set its chis to 40 and 75:
> swapaa ASP :41.a
> setattr a chi1 40 :41.a
> setattr a chi2 75 :41.a
> --Eric
>                        Eric Pettersen
>                        UCSF Computer Graphics Lab
>                        http://www.cgl.ucsf.edu
> On Jul 1, 2015, at 9:32 AM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:
>> Dear Alex,
>> Not directly, the “swapaa” command only uses the ranking rules that you tell it to use.  Only if the rules happened to choose that rotamer would you get it.  To directly choose a specific rotamer as listed in the rotamers dialog, you would have to use that dialog (Rotamers graphical user interface).
>> The rules are specified with the “criteria” option of swapaa, see:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html#criteria>
>> Rotamers graphical interface:
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html>
>> Best,
>> 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 Jul 1, 2015, at 4:57 AM, roz orchidea <roz.orchidea at gmail.com<mailto:roz.orchidea at gmail.com>> wrote:
>>> Dear all,
>>> I would like to use swapaa and choose which rotamer I want. Foe example I want from library dynameomics the second rotamer that appears in the pop-up menu of Arg. is it possible?
>>> Thank you for your time,
>>> Alex
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