Dear ChimeraX support team,
I tried the following command first - it worked well.
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match #1/A to #2/A
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Then I tried to align the two molecules using parts of them - it didn't work and complained that "No chains in reference structure PROT.pdb #2 compatible with BLOSUM-62 similarity matrix."
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matchmaker #1/A:10-20@CA to #2/B:10-20@CA
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System Info:
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