[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:

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

(b) Match->Align can make a multiple sequence alignment from multiple structures that are already superimposed

(c) Multalign Viewer has some editing features, such as adding a single sequence (with or without a structure) to an existing alignment

I hope this helps,
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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