[Chimera-users] swapaa: choosing rotamers

Eric Pettersen pett at cgl.ucsf.edu
Wed Jul 1 10:01:39 PDT 2015

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 Pettersen
                        UCSF Computer Graphics Lab

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
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