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$ gemmi convert -h
Usage:
gemmi convert [options] INPUT_FILE OUTPUT_FILE
with possible conversions between PDB, mmCIF and mmJSON.
FORMAT can be specified as one of: mmcif, mmjson, pdb, ccd (read-only).
ccd = coordinates of a chemical component from CCD or monomer library.
General options:
-h, --help Print usage and exit.
-V, --version Print version and exit.
-v, --verbose Verbose output.
--from=FORMAT Input format (default: from the file extension).
--to=FORMAT Output format (default: from the file extension).
CIF output options:
--style=STYLE one of: default, pdbx (categories separated with #),
aligned (left-aligned columns).
-b NAME, --block=NAME Set block name and default _entry.id
--sort Sort tags in alphabetical order.
--skip-category=CAT Do not output tags starting with _CAT
PDB input options:
--segment-as-chain Append segment id to label_asym_id (chain name).
--old-pdb Read only the first 72 characters in line.
-L, --force-label Add label_seq_id even if SEQRES is missing
PDB output options:
--short-ter Write PDB TER records without numbers (iotbx compat.).
--linkr Write LINKR record (for Refmac) if link_id is known.
--copy-remarks (pdb->pdb only) Copy REMARK records.
Any output options:
--minimal Write only the most essential records.
--shorten Shorten chain names to 1 (if # < 63) or 2 characters.
--rename-chain=OLD:NEW Rename chain OLD to NEW (--rename-chain=:A adds
missing chain IDs).
-s FILE Use sequence from FILE (PIR or FASTA format), which
must contain either one sequence (for all chains) or
as many sequences as there are chains.
--sifts-num Use SIFTS-mapped position in UniProt sequence as
sequence ID.
-B MIN[:MAX] Set isotropic B-factors to a single value or change
values out of given range to MIN/MAX.
--anisou=yes|no|heavy Add or remove ANISOU records.
--set-cispep Reset CISPEP records from omega angles.
Macromolecular operations:
--select=SEL Output only the selection.
--remove=SEL Remove the selection.
--apply-symop=OP Apply symmetry operation (e.g. '-x,y+1/2,-z'.
--expand-ncs=dup|num|x Expand strict NCS from in MTRIXn or _struct_ncs_oper.
New chain names are the same, have added numbers, or
the shortest unused names are picked.
--assembly=ID Output bioassembly with given ID (1, 2, ...).
--remove-h Remove hydrogens.
--remove-waters Remove waters.
--remove-lig-wat Remove ligands and waters.
--trim-to-ala Trim aminoacids to alanine.
When output file is -, write to standard output.
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