---
name: "pdbfixer"
section: "1"
platform: "linux"
package: "python3-pdbfixer"
version: "1.9-7"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pdbfixer"
---

# pdbfixer(1)

Fix problems in Protein Data Bank files

## 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