[Chimera-users] using modeller through chimera

[Elaine Meng]

On Oct 8, 2012, at 2:21 AM, Taufiq Rahman wrote:

> Just wonder whether in using modeller through Chimera interface, we can use our own alignment file or not.

Hi Taufiq,
Yes, you can definitely use your own alignment file -- just open it in Chimera.  To run Modeller using the Chimera interface, all you need is a sequence alignment of target and template (and if it has additional sequences, that is fine) plus the template structure, both opened in Chimera.  There are several ways of obtaining these inputs, outlined here:

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

See the third one, "using a pre-existing target-template sequence alignment"
Regards,
Elaine
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Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco