[chimerax-users] RMSD Problem

[Elaine Meng]

Hi Tim,
Well, the fix to this problem is given in the error message:  you need to specify the same numbers of atoms from the two models. :-)  But there are many potential issues to your question.

(A) Do you want to superimpose the models and then get the RMSD, or only get the RMSD in the current position?  If you want to superimpose them, use the  Matchmaker tool (menu Tools... Structure Analysis... Matchmaker) or command, e.g.

matchmaker #1 to #2

<https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

...which will report an alpha-carbon-only RMSD of paired residues in the Log.   The "align" command will also superimpose atomic structures but requires specifying the exact atoms to pair, and "rmsd" will calculate the RMSD in current positions without moving anything, and also requires specifying the exact atoms to pair.  Using "align" or "rmsd" it will be harder to come up with a correct command, since you will have to give the same numbers of atoms from each model.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html>

(B) Specifying atoms in the command line, e.g. for "align" or "rmsd": 
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

(1) when you give a residue number that means all of the atoms in the residue.  The problem is that different residues have different numbers of atoms in them.  Or even if the sequence is exactly the same and you expect the same number of atoms, maybe one structure is missing some of the atoms since they could not be resolved from the density.  For peptides with different sequences you may want to try using only CA atoms, or maybe only backbone atoms N,CA,C,O.  Some of the residues might be missing part of the backbone, however, and if so that would not solve the problem either.  

(2) I also can't tell if you really want the whole range of residues or not.  If you do want the whole range, you should use hyphens instead of commas.  Using a comma just gives a list of those two residues and not the ones in between.   If you really wanted the whole range, note that 149-264 is 116 residues whereas 469-553 is 85 residues, undoubtedly containing a different number of atoms. 

Let's pretend you want to measure RMSD in current positions (without moving the models) of only the two residues per model.  Then to specify backbone atoms only in those residues, you could try

rmsd #1:146,264 at n,ca,c,o to #2:469,553 at n,ca,c,o

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




> On Nov 8, 2022, at 3:06 AM, Timothy JM Clayson via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hiya, 
> 
> I am currently having a problem when trying to use RMSD on 2 sequences. 
> 
> I am using the command: 
> 
> rmsd #1:149,264 to #2:469,553
> 
> (where a.a. on chain 1 are 149-264 and on chain 2 they're 469-553)
> 
> It is coming up with the error:
> 
> 'Number of atoms from first atom spec (21) differs from number in second (10)'
> 
> I was wondering if there is a fix to this problem?
> 
> Thanks, 
> 
> Tim
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