Hi Dmitry, If you display only part of a map, for example by using the crop map mouse mode, or a command like volume #1 region 50,50,50,100,100,100, then if you use the ChimeraX save command it only saves that shown region. save mappiece.mrc model #1 You don't have to specify the "region" option when saving, and you don't need to use the volume copy command to save the cropped map. Tom
On Oct 25, 2023, at 9:34 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dmitry, You could create a copy of the map but only a region using "volume copy" with the "subregion" option to specify grid index ranges: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#copy>
Or, to save a map file with the smaller region, the "save" command allows specifying the map "region" by grid index ranges: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map>
(The current documentation also suggests you could also use a name for the region instead of the ranges, but I suspect that it is incorrect, so disregard that part.)
If you are using the "crop" mouse mode to interactively crop the map box, look in the Log: it will show a "volume" command with the "region" giving the indices you could use in the "volume copy" or "save" command.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2023, at 8:47 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
Could you advise on how to crop the map to the new 3D box size and save those changes?
Thank you.
Sincerely, Dmitry
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