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
--
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. <RMSD error.txt><RMSD bug.jpg><RMSD error.cxs><2nd fit RMSD.jpg>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/