[Chimera-users] rmsd calculation for pre aligned structures

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 2 13:33:57 PST 2015

Hi Oliver,
There isn't really any connection between mavRMSD and matchmaker.   You just need a sequence alignment associated with both structures (which I guess you were getting from Matchmaker), and then mavRMSD will show the actual separation between the residues in each column.  For example, if you then move one structure far away from the other, all the mavRMSD values will become high.

Instead of using Matchmaker to create the sequence alignment, you could open the two pre-aligned structures and then use Favorites… Sequence to show the sequence of one of them, and then from the sequence window (Multalign Viewer) menu, choose Edit… Add Sequence, From Structure (from the other structure) to create a two-sequence alignment.  Then just show the RMSD header of interest using the sequence window Headers menu.

You could use other ways of getting the sequence alignment.  If you already had a sequence alignment created outside of Chimera, you could just open it in Chimera and associate the two structures with the appropriate sequences, show RMSD header, etc.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 2, 2015, at 12:59 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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