Hey Roden,

If you color by chain, you'll see the issue. I think the rmsd you're getting is comparing chain A to chain A and chain B to chain B. Since A is aligned to B, the reported RMSD won't make sense. I guess you could rename the chains, or just use matchmaker to align them (mmaker #1 to #3).

Here's the description of rmsd from "help rmsd":
The two sets must contain the same number of atoms, which will be paired in the order given. If the order is not given explicitly, chains within a model are sorted by ID, residues with a chain sorted by number, and atoms within a residue sorted by name before pairing.
Harper
From: Roden Deng Luo via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Sent: Saturday, June 29, 2024 2:59 AM
To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] RMSD does not make sense in a few cases
 


Hello ChimeraX Team,

In the attached screenshot, #1 and #3 are almost overlapping, but get
an RMSD as 57. I occasionally encounter this. The session and log
files are attached. In short, to reproduce, open 5nl2.cif and
emd_3658.map; fitmap #1 in #2 search 1000; rmsd #1 to #3. This
happened rarely, but in this case, it happened twice. It might be that
I fit other structures first. But I indeed click "Clear List" and
"close session" after each fitting. The second top hit's RMSD seems to
make sense in the attached session (screenshot attached too).

Thanks,
Roden

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