$ servalcat fofc -h
usage: servalcat fofc [-h] [--halfmaps HALFMAPS HALFMAPS | --map MAP]
                      [--pixel_size PIXEL_SIZE] --model MODEL -d RESOLUTION
                      [-m MASK] [-r MASK_RADIUS] [-B B] [--half1_only]
                      [--normalized_map] [--no_fsc_weights]
                      [--sharpening_b SHARPENING_B] [--trim] [--trim_mtz]
                      [--monlib MONLIB] [--omit_proton] [--omit_h_electron]
                      [-o OUTPUT_PREFIX]

Fo-Fc map calculation based on model and data errors

optional arguments:
  -h, --help            show this help message and exit
  --halfmaps HALFMAPS HALFMAPS
  --map MAP             Use only if you really do not have half maps.
  --pixel_size PIXEL_SIZE
                        Override pixel size (A)
  --model MODEL         Input atomic model file
  -d RESOLUTION, --resolution RESOLUTION
  -m MASK, --mask MASK  mask file
  -r MASK_RADIUS, --mask_radius MASK_RADIUS
                        mask radius (not used if --mask is given)
  -B B                  Estimated blurring
  --half1_only          Only use half 1 for map calculation (use half 2 only
                        for noise estimation)
  --normalized_map      Write normalized map in the masked region
  --no_fsc_weights      Just for debugging purpose: turn off FSC-based
                        weighting
  --sharpening_b SHARPENING_B
                        Use B value (negative value for sharpening) instead of
                        standard deviation of the signal
  --trim                Write trimmed maps
  --trim_mtz            Write trimmed mtz
  --monlib MONLIB       Monomer library path. Default: $CLIBD_MON
  --omit_proton         Omit proton from model in map calculation
  --omit_h_electron     Omit hydrogen electrons from model in map calculation
  -o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
