[Chimera-users] matchmaker output

Tiziano Tuccinardi tiziano.tuccinardi at farm.unipi.it
Fri Mar 18 09:39:50 PDT 2011

Thanks Eric!!
It works very well!! Is it also possible to save the alignment file 
without omitting the all-gap columns?

Thanks again


Tiziano Tuccinardi, PhD

Dip. Scienze Farmaceutiche

Via Bonanno 6,

56126 PISA

Tel ++39 050 2219595

Fax ++39 050 2219605

E-mail tuccinardi at farm.unipi.it <mailto:tuccinardi at farm.unipi.it>


Adjunct Assistant Professor

SbarroInstitute for Cancer Research and Molecular Medicine

Centerfor Biotechnology


PhiladelphiaPA 19122 (USA)


Il 16/03/2011 22.23, Eric Pettersen ha scritto:
> 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.
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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