Oliver - Are you sure this makes sense? Per-residue RMSD values are sensitive to domain shifts because they are influenced by global rotation/translation and don't really represent per-residue structural similarity. Of course this depends on what you want to achieve - but you may be better of using a rotation/translation invariant metric based on internal coordinates: distance differences or torsion angle differences. Cheers, Boris On Mar 2, 2015, at 3:59 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi,
I have two structures that are pre-aligned in another program, and I would like to calculate a per-residue rmsd between the two structures and assign this to an attribute that I can use to color one of the structures.
Is there any way to do this at present?
The mavRMSD attribute only seems to be calculated after matchmaker, not after using the regular “rmsd” command.
Perhaps there is a way to do a dummy run of matchmaker, somehow forcing both structures to remain fixed?
Best, Oliver. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users