[Chimera-users] matchmaker output

Eric Pettersen pett at cgl.ucsf.edu
Wed Mar 16 14:23:19 PDT 2011

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:



                         Eric Pettersen
                         UCSF Computer Graphics Lab

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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