NAME

       pdbfixer - Fix problems in Protein Data Bank files

SYNOPSIS

       pdbfixer

DESCRIPTION

              pdbfixer filename [options]

       When  run  with no arguments, it launches the user interface.  If any arguments are specified, it runs in
       command line mode.

OPTIONS

       -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

pdbfixer 1.9                                      February 2025                                      PDBFIXER(1)