[Chimera-users] swapaa: choosing rotamers

[roz orchidea]

I will try it! Thanks a lot!

2015-07-09 14:43 GMT+02:00 Repic Matej <matej.repic at epfl.ch>:

>  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')
>  """
>
>  Best,
> Matej
>
>  ---------------------------------
>  Dr. Matej Repic
>  Ecole Polytechnique Fédérale de Lausanne
> Laboratory of Computational Chemistry and Biochemistry
> SB - ISIC – LCBC
> BCH 4108
> CH - 1015 Lausanne
>  ------------------------------------------------------
>
>   From: <chimera-users-bounces at cgl.ucsf.edu> on behalf of roz orchidea <
> roz.orchidea at gmail.com>
> Date: Thursday, July 9, 2015 at 12:49
> To: "chimera-users at cgl.ucsf.edu" <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,
>  Alex
>
> 2015-07-01 19:03 GMT+02:00 Eric Pettersen <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
>>
>> --Eric
>>
>> On Jul 1, 2015, at 10:01 AM, Eric Pettersen <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> 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>
>> 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
>> >>
>> >>
>> >> _______________________________________________
>> >> Chimera-users mailing list
>> >> Chimera-users at cgl.ucsf.edu
>> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> >>
>> >
>> >
>> >
>>
>>
>
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