rmsz-help.txt

$ gemmi rmsz -h
Usage:
 gemmi rmsz [options] [FILE]...

Validate geometry of a coordinate file with (Refmac) monomer library.

Options:
  -h, --help         Print usage and exit.
  -V, --version      Print version and exit.
  -v, --verbose      Verbose output.
  -q, --quiet        Show only summary.
  --monomers=DIR     Monomer library directory (default: $CLIBD_MON).
  -L CIF, --lib=CIF  User's restraint file(s). See more info below.
  --format=FORMAT    Input format (default: from the file extension).
  --cutoff=ZC        List bonds and angles with Z score > ZC (default: 2).
  -s, --sort         Sort output according to |Z|.
  --missing          List missing atoms.

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