pdbfixer - Fix problems in Protein Data Bank files
- pdbfixer filename [options]
When run with no arguments, it launches the user interface. If any
arguments are specified, it runs in command line mode.
- -h, --help
- show this help message and exit
- --pdbid=PDBID
- PDB id to retrieve from RCSB [default: None]
- --url=URL
- URL to retrieve PDB from [default: None]
- --output=FILENAME
- output pdb file [default: output.pdb]
- --add-atoms=ATOMS
- which missing atoms to add: all, heavy, hydrogen, or none [default:
all]
- --keep-heterogens=OPTION
- which heterogens to keep: all, water, or none [default: all]
- --replace-nonstandard
- replace nonstandard residues with standard equivalents
- --add-residues
- add missing residues
- --water-box=X
Y Z
- add a water box. The value is the box dimensions in nm [example:
--water-box=2.5 2.4 3.0]
- --ph=PH
- the pH to use for adding missing hydrogens [default: 7.0]
- --positive-ion=ION
- positive ion to include in the water box: Cs+, K+, Li+, Na+, or Rb+
[default: Na+]
- --negative-ion=ION
- negative ion to include in the water box: Cl-, Br-, F-, or I- [default:
Cl-]
- --ionic-strength=STRENGTH
- molar concentration of ions to add to the water box [default: 0.0]
- --verbose
- Print verbose output