[BiO BB] Help with RMSD calculation

Dr. Christoph Gille christoph.gille at charite.de
Wed Aug 2 08:26:01 EDT 2006

> Does anyone have a script or algorithm that can calculate the minimum
> RMSD if C-alpha co-ordinates of two protein fragments are given? I
> mean, the algorithm should rotate and translate the first set of
I recommend TM_align, which is a fast Fortran program.
I have a Java wrapper which takes care of downloading, compiling the Fortran
and executing. You can also use CE/CL. But this is slower and the user
interface is more difficult. I have also a Java interface for CE.

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