[Owl-devel] Question about T-Coffee

[Dan Bolser]

Cheers Henning,

Tom, you can find the SVN repo for the project [1] here:

http://www.bioinformatics.org/websvn/listing.php?repname=owl


I think the point of using T-Coffee is to use a measure that is a bit
more sensitive than RMSD.


Thanks for the query reply,
Dan.

[1] http://www.bioinformatics.org/project/?group_id=1014


On 11 March 2010 16:09, Henning Stehr <stehr at molgen.mpg.de> wrote:
>
> Indeed it was. Have a look at owl.sequence.TCoffeeRunner. It only
> parses the alignment output from TCoffee though. I'm not quite sure
> what you or your colleague exactly want to do but if you want to
> calculate minimum RMSD superimpositions of multiple structures, I'm
> using the Polypose tool from CCP4. The Java wrapper is
> owl.proteinstructure.PolyposeRunner. The method
> PolyposeRunner.executePolypose(...) returns an RMSD.
>
> Cheers,
> Henning
>
> On Thu, Mar 11, 2010 at 4:58 PM, Dan Bolser <dan.bolser at gmail.com> wrote:
> > Was TC ever part of the structure prediction pipeline?
> >
> > A colleague here would like to use it to calculate iRMSD (or some similar
> > statistics).
> >
> > Cheers,
> > Dan.
> >
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> >