crd-help.txt

$ gemmi crd -h
Usage:
 gemmi crd [options] INPUT_FILE OUTPUT_FILE

Prepare intermediate Refmac files.
INPUT_FILE can be in PDB, mmCIF or mmJSON format.

Options:
  -h, --help          Print usage and exit.
  -V, --version       Print version and exit.
  -v, --verbose       Verbose output.
  --monomers=DIR      Monomer library directory (default: $CLIBD_MON).
  -L CIF, --lib=CIF   User's restraint file(s). See more info below.
  --auto-cis=Y|N      Assign cis/trans ignoring CISPEP record (default: Y).
  --auto-link=Y|N     Find links not included in LINK/SSBOND (default: N).
  --auto-ligand=Y|N   If ligand has no definition make ad-hoc restraints (N).
  --no-aliases        Ignore _chem_comp_alias.

Hydrogen options (default: remove and add on riding positions):
  -H, --no-hydrogens  Remove (and do not add) hydrogens.
  --keep-hydrogens    Preserve hydrogens from the input file.

Option -L/--lib can be used multiple times, in order of priority.
Its argument is either a file path or one of the two special values:
    '+' = monomer blocks in mmCIF INPUT_FILE (ignored by default)
    '@' = the priority of the monomer library (ML, default: lowest)
Example 1:   -L file.cif -L+    order: file.cif, input file, ML
Example 2:   -L@ -L file.cif    order: ML, file.cif