$ servalcat trim -h
usage: servalcat trim [-h] [--maps MAPS [MAPS ...]] [--mask MASK]
                      [--pixel_size PIXEL_SIZE] [--model MODEL [MODEL ...]]
                      [--no_expand_ncs] [--padding PADDING]
                      [--mask_cutoff MASK_CUTOFF] [--noncubic] [--noncentered]
                      [--no_shift] [--no_shift_keep_cell]
                      [--force_cell FORCE_CELL FORCE_CELL FORCE_CELL FORCE_CELL FORCE_CELL FORCE_CELL]
                      [--disable_cell_check] [--shifts SHIFTS]

Trim maps and shift models into a small new box.

optional arguments:
  -h, --help            show this help message and exit
  --maps MAPS [MAPS ...]
                        Input map file(s)
  --mask MASK           Mask file
  --pixel_size PIXEL_SIZE
                        Override pixel size (A)
  --model MODEL [MODEL ...]
                        Input atomic model file(s)
  --no_expand_ncs       Do not expand strict NCS in MTRIX or _struct_ncs_oper
  --padding PADDING     padding in angstrom unit (default: 10.0)
  --mask_cutoff MASK_CUTOFF
                        Mask value cutoff to define boundary (default: 0.5)
  --noncubic
  --noncentered         If specified non-centered trimming is performed. Not
                        recommended if having some symmetry
  --no_shift            If specified resultant maps will have shifted origin
                        and overlap with the input maps.
  --no_shift_keep_cell  Keep original unit cell when --no_shift is given
  --force_cell FORCE_CELL FORCE_CELL FORCE_CELL FORCE_CELL FORCE_CELL FORCE_CELL
                        Use specified unit cell parameter
  --disable_cell_check  Turn off unit cell consistency test
  --shifts SHIFTS       Specify shifts.json to use precalculated parameters

If --mask is provided, a boundary is decided using the mask and --padding.
Otherwise the model is used.
