[Chimera-users] per-residue "RMSD" values from alignment

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 7 13:02:56 PST 2019

Hi Vito,
(I changed the subject line because “Question” is not useful to people searching the chimera-users archive.)

You can save the per-residue “RMSD” values to a text file.  Since you have only two structures, the values are just the distance between the two CA atoms in that column of the sequence alignment.

The RMSD values in the histogram above the sequences in Multalign Viewer are assigned as an attribute to the structure residues in each column, as explained here:

You can write attribute values to file using Render by Attribute (Tools… Depiction… Render by Attribute).  In that tool’s menu, choose “File.. Save Attribute” and then specify which attribute to save.  

You want the attribute of “residues” named “mavRMSDca” (the “mav” part means that it comes from Multalign Viewer).  In the “Models” section at the top of that dialog, you could just choose one model or the other to report the values with its residue numbers.  If you choose both models, then you will get each distance twice because there are two residues (one from each structure) for each alignment column with the value.

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

> On Feb 7, 2019, at 3:04 AM, Vito Calderone <calderone at cerm.unifi.it> wrote:
> I have superposed two structures and printed the attached figure with sequence superposition and Ca RMSD.
> Is there a list of residue by residue RMSD as well? I can’t find it anywhere apparently.
> Thanks
> Vito

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