If this is from a 3D map, it can also involve masking the map around the model, using a command as follows:
volume zone #2 near #4 range 2 new true
#2 is the map to mask
#4 is the model with atoms - could be ’sel’ as well if you have the atoms of interest selected
Type ‘help volume zone’ for more details on the other params
Be careful with the contour level of this masked map, should not be too low to the point where noise would be shown in the original map, although it is usually obvious when this is the case, because the contour is not as smooth as in the image you show.
Greg P.
On Jun 17, 2025, at 5:36 PM, Das, Abhinaba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: