[Chimera-users] how to make super8.msf.

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 21 10:35:55 PDT 2013


Hi Han,
The super8.msf file was not made in Chimera.  For the other people on the list:  that file is a multiple sequence alignment linked to the "Sequences and Structures" tutorial in the Chimera User's Guide.  I got it from someone several years ago; I believe it was edited manually in a text-editor after initial creation in some other program.

For making multiple sequence alignments, there are far too many programs for me to list.  However, I have a web page that lists a sample of databases and web services that can be used as sources of multiple sequence alignments:
<http://www.cgl.ucsf.edu/home/meng/sources.html>

Chimera focuses more on structure-sequence linkage than on sequence-only data, but here are some related features:

(a) MatchMaker can make a pairwise sequence alignment from two related structures
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>

(b) Match->Align can make a multiple sequence alignment from multiple structures that are already superimposed
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html>

(c) Multalign Viewer has some editing features, such as adding a single sequence (with or without a structure) to an existing alignment
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#editing>

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 Mar 20, 2013, at 10:40 PM, han xiaodon wrote:

> dear professor. would you share me how to make super8.msf.




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