[Chimera-users] Question about multi align viewer

[Elaine Meng]

On Sep 20, 2013, at 9:33 AM, Sean Connell wrote:

> Hello I was wondering if it is possible to calculate conservation statistics using only subsets of the aligned sequence.  The reason I ask is that in my alignment I have differently families of proteins that have slightly different functions and I would like to highlight residues that are conserved in one subset but not in the other?
> 

Hi Sean,
Not directly.  I believe you would have to create alignments of just those subsets.  You could do that with some other program (including text-editor) before opening the alignment in Chimera, or you could do it in Chimera.  Of course, keep the original file with the full alignment too! To edit in Chimera, open the full alignment and then from the sequence window menu choose "Edit... Delete Sequences/Gaps" and in the resulting dialog, choose which sequences to delete.  

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavmenu-edit>

You can then continue working with the subset alignment in Chimera, including saving it to a new file (sequence window menu "File... Save As").
I hope this helps,
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

P.S. your original message was in an attachment, which was kind of weird, but I could view it by just clicking the attachment