When I tried it (e.g. volume copy) the region was exactly superimposed on the same part of the original map, see attached image.  

Maybe you moved one map separately from the scene, such as to fit it to another?  If so, you could try applying its transformation to the other one with "view position" using the "sameAsModels" option:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#position>

I hope this helps,

Elaine

On Oct 25, 2023, at 9:54 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

thank you, Elaine,

It worked but the newly created map was shifted away from the Origin one.

What I am aiming for is to crop the Original map together with the box size, but the new smaller map with the smaller box size was still in the center. In the sketch below I need to get the orange cylinder (168x168x168) from the Origin blue cylinder (384x384x384).
So when I open the orange and the blue maps both cylinders overlap.


Is there such an option in ChimeraX? 


Thank you in advance.

Sincerely,
Dmitry

<image.png>
From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: 25 October 2023 17:34
To: Dmitry Semchonok <semchonok@gmail.com>
Cc: ChimeraX <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] crop the map
 
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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