[Chimera-users] rmsd calculation for pre aligned structures

Boris Steipe boris.steipe at utoronto.ca
Mon Mar 2 13:53:34 PST 2015


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 at 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.
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