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.