Hi Guillame, You can make a map with "volume zone" and then subtract the zone from the original map with "volume subtract" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#subtract> Or you can use "volume mask" to zero out parts inside or outside of a surface <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask> You can place markers manually at map density maxima, see the Marker Placement tool: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html> ...and associated mouse modes <https://rbvi.ucsf.edu/chimerax/docs/user/tools/markers.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 Apr 24, 2024, at 12:44 PM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
With `volume zone` I can show the parts of a map close to an atomic model. Is there a way to do the opposite, i.e. show only the parts of a map that don’t enclose any atoms?
This would be already very helpful only as a visualization. But even better would be a way to build a list of markers at the centroids of such unmodeled blobs, to easily navigate to them. Or maybe this is too narrow in scope and better left to ISOLDE? (Sorry Tristan… more feature suggestions…).
Thank you,
Guillaume