[Owl-devel] Question about T-Coffee

[Henning Stehr]

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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