HI Roden,
The "rmsd" command works fine -- you just have to specify in the command which atoms to use instead of the whole models, for example:

rmsd #2:10-500@ca to #3:10-500@ca

... or maybe their residue numbers are different too, e.g.

rmsd #2:14-353@n,ca,c,o  to #3:12-351@n,ca,c,o

See help on rmsd
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html__;!!Nmw4Hv0!0dK60YHtglh6C6j_LaMD1eyVp2A_KI6HAPhKr2i4nnXsHezoAmHdV3tb8qZuptvD1CpHyyuByFIrr4uH9CVB$ >

See help on command-line specification of atoms, residues, chains, etc.
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html*hierarchy__;Iw!!Nmw4Hv0!0dK60YHtglh6C6j_LaMD1eyVp2A_KI6HAPhKr2i4nnXsHezoAmHdV3tb8qZuptvD1CpHyyuByFIrrwtYIb4H$ >

The main thing is that you have to figure which atoms go with which atoms yourself, instead of like matchmaker where it figures it out for you.  Also matchmaker only uses CA atoms for the reported RMSD, so maybe you want to use more atoms.

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


> On Nov 24, 2024, at 11:23 PM, Roden Deng Luo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hi,
>
> If two atomic models do not have the exact same atoms, rmsd command does not run. One workaround would be to use matchmaker beforehand, and there is indeed a reported RMSD between "pruned atom pairs." However, this applies the matching before the calculation. In addition, from the attached screenshot (matching https://urldefense.com/v3/__https://alphafold.ebi.ac.uk/files/AF-P32565-F1-model_v4.cif__;!!Nmw4Hv0!0dK60YHtglh6C6j_LaMD1eyVp2A_KI6HAPhKr2i4nnXsHezoAmHdV3tb8qZuptvD1CpHyyuByFIrr94jqUkJ$  to 5wvi chain N), I expect most of the atoms should not be pruned, which is not the case.
>
> I wonder if there is a command or tool to calculate the RMSD between the not-moved nonidentical atomic models.
>
> Thanks,
> Roden
>
>
>
>
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