Hi Abhi, Well, with "volume zone" you can make a new map with zeroes beyond some cutoff distance of the atom positions. However, that seems a bit circular if the point is to fit the atoms again. I guess you could use a large-ish cutoff distance. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone> Since you fit the atoms into the map, the map grid would retain its original coordinates and the new edited map would just use that same grid. I.e., if I understand correctly, there isn't an issue of preserving the map position, since it was the atomic structure that was repositioned, not the map. If the atomic structure is not occupying the entire asymmetric unit of the map (say there are other protein or nucleic acid chains also in the AU but explicitly present as atomic structures), however, the approach above would not be useful. There are other ways to crop out parts of the map, such as by drawing a rectangular box manually (or specifying that region directly in a "save" map command) or using the Map Eraser tool to erase inside a sphere that can be moved with the mouse. See: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#erase> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/maperaser.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 23, 2024, at 1:57 PM, Das, Abhinaba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi!

I was wondering if there is a sequence of commands one could use to extract an asymmetric unit from the original map after roughly fitting the model into it. The positions of these extracted maps should of course be preserved and should on the same grid. One can then better fit the model in this extracted ASU density.

Thanks in advance for any guidance. Abhi