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