Aha! Thanks, Tom! I will then use the following command to turn the molecule and calculate a working RMSD in such cases. Kindly correct me if I'm wrong. turn z 1 180 model #1 center #1 coordinateSystem #1 Best, Roden On Sat, Jun 29, 2024 at 7:01 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Roden,
PDB 5nl2 is symmetric and when you fit it to a map and it is flipped 180 degrees you get an RMSD of 57 Angstroms.
Tom
On Jun 28, 2024, at 11:59 PM, Roden Deng Luo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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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