Hello,
My guess is that this has nothing to do with display, but instead that some atoms are outside the entire rectangular box of your volume data grid.  Probably you just need to extend the box (based on the periodicity of the map) to cover the atoms, which can be done with command "volume cover", see:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#cover>

As far as I know there would not be a zone on the map unless you have previously applied "volume zone" or the corresponding toolbar icon or mouse mode:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone>

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 Jul 1, 2025, at 9:35 AM, Murpholino Peligro via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear all
> I got a pdb and a mtz file (from phenix.maps) with:
>
>     Number of columns: 11
>     label          #valid  %valid     min     max type
>     H               23487 100.00%    0.00   56.00 H: index h,k,l
>     K               23487 100.00%    0.00   39.00 H: index h,k,l
>     L               23487 100.00%    0.00   26.00 H: index h,k,l
>     2FOFCWT         23337  99.36%    0.01 1113.30 F: amplitude
>     PH2FOFCWT       23337  99.36% -180.00  180.00 P: phase angle in degrees
>     2FOFCWT_fill    23487 100.00%    0.01 1113.30 F: amplitude
>     PH2FOFCWT_fill  23487 100.00% -180.00  180.00 P: phase angle in degrees
>     FOFCWT          23337  99.36%    0.00  836.89 F: amplitude
>     PHFOFCWT        23337  99.36% -180.00  180.00 P: phase angle in degrees
>     ANOM            19860  84.56%    0.00  149.58 F: amplitude
>     PHANOM          19860  84.56% -179.97  179.99 P: phase angle in degrees
>
> (as reported by phenix.mtz.dump)
> I open both in chimerax with
> open /home/murph/doc/pdbs/mol1/mol1.pdb
> open /home/murph/doc/pdbs/mol1/mol1_map_coeffs.mtz structureModel #1
> (clipper already installed)
> If I do tools->structure analysis->check waters
> and choose the model (now id #1.2) and the 2fofc map (#1.1.1.2) I got a warning saying "Some (or all) atoms lie outside the volume, continue anyway?" If I continue anyway... some waters with density do have a 0 in the density column...
>
> This is, I think, because by default the density is not displayed around all atoms of the model (huge models would crash the computer, right?).. so maybe I just need to show the density around all the atoms in the model... How do I do that? (I thought that 'volume unzone' was the magic command but that only shows a bigger cube of density around the center of rotation, instead of the smaller sphere of density).
>
> Thanks
>
>
>
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