Hi Yanhe,

  The ChimeraX clip plane is just a graphical hiding of part of the map.  It doesn't allow you to save just the displayed part.  For that you would crop the map, for instance with the "region" option of the volume command or the "Crop" mouse mode, then save the map which will save just the cropped region.  But that only allows cropping along x, y or z axes not with a tilted plane.  If you wanted to save a map after cutting along a tilted plane you would probably need to resample the map with on a rotated grid (volume resample command) so the z axis perpendicular to the plane you want and then use the "region" option.  Resampling will degrade the resolution so you don't want to do that if you intend to do analysis on the tilted axis cropped map.

        Tom


> On Feb 20, 2025, at 2:43 PM, Yanhe Zhao via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Greeting there ChimeraX developer and community,
>
> I have "clip" used on my map and currently want to save the clipped one as a new mrc file, what is the best way to do this?
> I checked the "save Map" command and found the region option, but I don't think it is the right option if I have my clip plan tilt.
> Thanks a lot for any input.
>
> Thanks and cheers,
> Yanhe
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