[chimerax-users] matchmaker RMSD in ChimeraX

[Elaine Meng]

Hi Martin,
Matchmaker reports RMSD over all the paired positions, as you said, but not per residue.  Since matchmaker is pairwise, however, the “RMSD” per position is simply the distance between the two alpha-carbons. In ChimeraX, you could just measure all the pairwise CA-CA distances using “distance” commands.  If the numbering in the two sequences is the same, it would be pretty easy to script, possibly even as a single iterative “perframe” command with the “distance” command embedded.  If the numbering in the two sequences is different, then it would be more of a pain.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html>

For example, with 2gbp matched to identically numbered 2fw0, I could use:
perframe "distance /a:$1 at ca /a:$1 at ca" range 2,306
distance save /path/my-distances/file

That would measure the distances for ALL positions in the range 2-306.  Note, however, that matchmaker default is to not use all the positions to superposition the proteins, but exclude (prune) the far-apart positions from the final fit.  The light orange blocks in the shown pairwise alignment indicate which columns are actually used in the final fit and reported overall RMSD.  

To report overall RMSD from all positions without pruning, you’d either have to turn off pruning in matchmaker (which would generally give a worse fit), or keep the matchmaker superposition the same but then use a separate “align” command with “move nothing” option afterwards.  Remember to specify only the desired atoms, e.g. @ca, in that command.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>

You could resort to using Chimera:  matchmaker with “showAlignment true” and then in the resulting sequence alignment, show the desired RSMD header from its headers menu, then use Render by Attribute (under Tools… Depiction in the menu) to save a text file of the corresponding mavRMSD[…] attribute.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#assessment>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving>

When ChimeraX has RMSD headers on sequence alignments and saving attributes to file, then you would use a similar process in ChimeraX.  However, those functions are not yet available.

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

> From: Martin Moncrieffe <mcm35 at cam.ac.uk>
> Date: March 4, 2019 at 1:15:06 AM PST
> To: Tom Goddard 
> Subject: matchmaker in ChimeraX
> 
> Hi Tom,
> 
> Is it possible to get the rmsd as a function of residue position when using mm in ChimeraX? I’ve turned on the verbose flag and can see the residues used to match but not their respective rmsd’s. 
>