Dear Avner, You can create a multiple sequence alignment from a multiple structure alignment using "Match -> Align" (under Tools... Structure Comparison). In the production release of Chimera (Dec 2008, version 1.3) it simply uses the current structure alignment: <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/ matchalign/matchalign.html> In newer versions (if you get a recent daily build of Chimera), it can also iterate to improve the result by creating a sequence alignment, refitting, creating a new sequence alignment (etc.): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/ matchalign.html> It sounds like you superimposed the structures using MatchMaker, which makes a separate sequence alignment for each pair. If the structures are now superimposed the way you want, you can Quit from each of those pairwise sequence alignments to delete them, then use Match -> Align to create a new multiple sequence alignment. That alignment (like the pairwise ones) will be shown automatically in Multalign Viewer. You can save it to a file using "File... Save As" in the Multalign Viewer menu. The "superpositions and alignments" tutorial includes using MatchMaker and Match -> Align: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ alignments.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On May 8, 2009, at 12:33 PM, Avner Schlessinger wrote:

Dear Chimera experts,

Once I create multiple structure alignment i was wondering how I can view the corresponding multiple sequence alignment. when I try to view it through the MultiAlignViewer it shows all possible pairwise alignments with the sequence of the first structure rather than all the sequences together.

Thanks! Avner