$ gemmi sfcalc -h
Usage:
  gemmi sfcalc [options] INPUT_FILE

Calculates structure factors of a model (PDB, mmCIF or SMX CIF file).

Uses FFT to calculate all reflections up to requested resolution for MX
files. Otherwise, for SMX and --hkl, F's are calculated directly.
This program can also compare F's calculated directly with values
calculated through FFT or with values read from a reflection file.

Options:
  -h, --help           Print usage and exit.
  -V, --version        Print version and exit.
  -v, --verbose        Verbose output.
  --hkl=H,K,L          Calculate structure factor F_hkl.
  --dmin=NUM           Calculate structure factors up to given resolution.
  --for=TYPE           TYPE is xray (default), electron, neutron or mott-bethe.
  --normalize-it92     Normalize X-ray form factors (a tiny change).
  --use-charge         Use X-ray form factors with charges when available.
  --ciffp              Read f' from _atom_type_scat_dispersion_real in CIF.
  --wavelength=NUM     Wavelength [A] for calculation of f' (use --wavelength=0
                       or -w0 to ignore anomalous scattering).
  --unknown=SYMBOL     Use form factor of SYMBOL for unknown atoms.
  --noaniso            Ignore anisotropic ADPs.
  --margin=NUM         For non-crystal use bounding box w/ margin (default: 10).

Options for density and FFT calculations (with --dmin):
  --rate=NUM           Shannon rate used for grid spacing (default: 1.5).
  --blur=NUM           B added for Gaussian blurring (default: auto).
  --rcut=Y             Use atomic radius r such that rho(r) < Y (default: 1e-5).
  --test[=CACHE]       Calculate exact values and report differences (slow).
  --write-map=FILE     Write density (excl. bulk solvent) as CCP4 map.
  --to-mtz=FILE        Write Fcalc to a new MTZ file.

Options for anisotropic scaling (only w/ FFT):
  --scale-to=FILE:COL  Anisotropic scaling to F from MTZ file.
                       Argument: FILE[:FCOL[:SIGFCOL]] (defaults: F and SIGF).
  --sigma-cutoff=NUM   Use only data with F/SIGF > NUM (default: 0).

Options for bulk solvent correction and scaling (only w/ FFT):
  --d-mask=NUM         Spacing of mask grid (default: same as for model).
  --radii-set=SET      Set of per-element radii, one of: vdw, cctbx, refmac.
  --r-probe=NUM        Value added to VdW radius (default: 1.0A).
  --r-shrink=NUM       Value for shrinking the solvent area (default: 1.1A).
  --solvent-mask=FILE  Use mask from file instead of calculating it.
  --ksolv=NUM          Value (if optimizing: initial value) of k_solv.
  --bsolv=NUM          Value (if optimizing: initial value) of B_solv.
  --kov=NUM            Value (if optimizing: initial value) of k_overall.
  --baniso=B11:...:B23 Anisotropic scale matrix (6 colon-separated numbers: B11,
                       B22, B33, B12, B13, B23).

Options for comparing calculated values with values from a file:
  --compare=FILE       Re-calculate Fcalc and report differences.
  --f=LABEL            MTZ column label (default: FC) or small molecule cif tag
                       (default: F_calc or F_squared_calc).
  --phi=LABEL          MTZ column label (default: PHIC).
