[Chimera-users] Modeller-Chimera interface

[Elaine Meng]

Hi James,
Yes, you can specify multiple templates in the Modeller interface -- you must have those structures already open in Chimera before you can choose them in the dialog.  It doesn't matter where the sequence alignment came from: you just need to have it open in Chimera and associated with the structure(s), also open in Chimera, that you want to use as template(s).  Click the Help button on the Modeller dialog or see documentation here:

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative>

... and here is a little more about sequence-structure association in Chimera:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association>

I would only note that if your sequence alignment is huge (has lots of sequences), it may be quite slow to interact with it in Chimera.

I hope this helps,
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 Sep 20, 2012, at 7:08 AM, James Valdes wrote:

> Hello Chimera,
> I'm using the Modeller interface via Chimera and I was wondering if
> the models produced takes into account multiple templates (e.g.,
> selecting all) from a multiple alignment produced by MAFFT
> (http://mafft.cbrc.jp/alignment/software/). I appreciate any insight
> you may provide.
> Cheers,
> James Jason Valdés, Ph.D.