Hi Roden, I think you can run "fitmap" but without moving the atoms by using options "shift false" and "rotate false" ... that will report the fitmap result. However, most of the metrics are for map-map fitting - what you get for atoms-map fitting may just be the average value of the map at atom positions. It might also say how many atoms are inside the map contour surface. Or, you can use the "resolution" option to make a map from the atoms and then get the map-map metrics like correlation. See "fitmap" and options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 5, 2024, at 8:58 AM, Roden Deng Luo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi ChimeraX Team,
I wonder if there is a command that can measure the fit quality of an atomic structure to a volume map. I imagine the metric could be the sum of the density of all atoms or a correlation. Something like: fit_quality #ModelID in #VolumeID (similar to: rmsd #1 to #2).
Thanks, Roden