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$ gemmi prep -h
Usage:
gemmi prep [options] INPUT_FILE OUTPUT_FILE
gemmi prep --split [options] INPUT_FILE OUTPUT_BASENAME
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.
--split Split output into two files: crd and rst.
--monomers=DIR Monomer library dir (default: $CLIBD_MON).
--libin=CIF Custom additions to the monomer library.
--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).
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.
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