[Chimera-users] matchmaker output
tiziano.tuccinardi at farm.unipi.it
Fri Mar 18 09:39:50 PDT 2011
It works very well!! Is it also possible to save the alignment file
without omitting the all-gap columns?
Tiziano Tuccinardi, PhD
Dip. Scienze Farmaceutiche
Via Bonanno 6,
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
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:
> 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.
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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