[Chimera-users] Question about multi align viewer

Jim Procter jprocter at compbio.dundee.ac.uk
Thu Oct 3 03:33:28 PDT 2013

Hello Sean, and Elaine.

This is a bit late - but I thought I'd plug Jalview here since subfamily 
conservation is one of its key features. Although it doesn't (yet) link 
directly with Chimera, it is straightforward to visualize subfamily 
conservation and export it as a CSV.

You can see how it has been used in this paper by Chen et al (2012) :

If you want a less interactive - but phylogenetically rigorous approach, 
you should check out ConSurf - whose results Chimera can directly 
display ( http://www.cgl.ucsf.edu/chimera/consurf/consurf.html ).

Hope this helps too!

ps. as an aside - I'm working on having Chimera linked with Jalview 
sometime before the end of this year, which would allow you to 
interactively highlight conserved residues within subfamilies. Drop me a 
line if you are interested in test driving this!

On 20/09/2013 17:41, Elaine Meng wrote:
> 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
> -----
> 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
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