On Mar 16, 2011, at 6:30 AM, Tiziano Tuccinardi wrote:

Dear all,
I am using MatchMaker for aligning about 100 structures, and it works very well!!
Is it possible to automatically save the pairwise alignment without opening the MultAlignViewer? Due to the large number of structures, I cannot use the Match-Align tool but it would be enough to save the pairwise alignments

Hi Tiziano,

Sorry about Match-Align not being practical for large numbers of structures.  It's written entirely in Python and it would be nice if I could move it to C++, but it's pretty complicated and there are always many other priorities...

And then there's MultAlign Viewer, which was written many moons ago before we realized how important it was to have command line access to all parts of Chimera.  So you can get the end result you want but you do have to open an MAV for each pairing and then run a script after all the pairings are done that will get each of those MultAlign Viewer instances to save their alignment.  I have attached a script file for that.  You run the script with the "runscript" command, specifying the folder where you want the alignments saved, and the alignment format.  You run it like this:

runscript <folder-with-script>/save-alignments.py save-folder-path "Clustal ALN"

The possible alignment formats are listed in the "Sequence Alignments" table here:

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu

P.S. Right now the runscript command doesn't handle "~"-expansion-to-home-dir correctly, but will in the next daily build and in the upcoming 1.5.3 release.

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