Dear Ahmed,

ChimeraX does not calculate TM-Score.  You can calculate RMSD, but of course it depends on how the structures are superimposed. 

The Matchmaker tool and command will do the superposition and also report an RMSD, but the fitting and RMSD only use the CA atoms that were paired by sequence alignment.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

If you need to use more atoms for superposition, see the "align" command:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>

If  the structures are already superimposed, you can calculate RMSD over specified atoms using the "rmsd" command:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html>

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