[Chimera-users] swapaa: choosing rotamers

[Elaine Meng]

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