[Chimera-users] swapaa: choosing rotamers

[roz orchidea]

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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