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