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Hello Poonam Dhindwal,
Firstly, you should know that RMSDca is just the same thing as the simple CA-CA distance when you have only two structures. If you choose RMSD: backbone or RMSD: full it will use more atoms from the two residues at each position.  See "RMSD headers"
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To save it there are a couple of different approaches depending on what you want.

(A) You can use the sequence window menu Headers... Save and it will have a choice to save the RMSD values along with their positions in the alignment.

For details about headers (lines above the alignment) and header files, see
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(B) Alternatively, if you want the header values vs. amino acid residue numbering in the structure (either one or both, whichever you prefer), you can instead use main menu Tools... Structure Analysis... Render by Attribute to save an attribute assignment file.  In that Render by Attribute tool, use its menu File... Save Attributes.  Then in the attribute saving dialog, choose the model (which structure) and choose attribute of "residues" and then choose Attribute: "mavRMSDca "

See saving attributes and attribute file format
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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 Jan 16, 2024, at 9:14 AM, Dhindwal, Poonam via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Hello,
> I was wondering if there is a way in Chimera to generate RMSD values for individual C alpha after structure alignment. I want to plot a graph of RMSD vs individual Amino acids. I performed 'Matchmaker' to generate the structure alignment and in the output tab, I can see rmsd bars on top of aligned sequences but I am unable to get the exact values of RMSD.
>
> Any help would be greatly appreciated.
>
> Thank you,
>
> Poonam Dhindwal, Ph.D.