PDB file reader

For loading model structures stored in the RCSB Protein Data Bank (PDB) format. OVITO can directly load gzipped PDB files (“.gz” suffix).

Options

Generate bounding box if needed

If this option is enabled and no simulation cell is found in the PDB file (no CRYST1 record), OVITO will generate an axis-aligned bounding box containing all atoms. This bounding box has open boundary conditions and can be used as an approximate simulation cell in subsequent calculations.

Center simulation cell on coordinate origin

If enabled, OVITO shifts the geometric center of the simulation cell to the origin of the coordinate system, including all atoms. Otherwise, the simulation cell is positioned such that its corner is located at the coordinate origin.

Generate distance-based bonds

Lets OVITO create ad-hoc bonds between atoms based on their van der Waals radii. This is equivalent to inserting a Create bonds modifier into the pipeline.

Load bonds from file

Tells OVITO to read pair-wise connections from the input file. These are identified by the CONECT record in the PDB file.

Python parameters

The file reader accepts the following optional keyword parameters in a call to the import_file() or load() Python functions.

import_file(location, sort_particles=False, bounding_box=False, centering=False, generate_bonds=True)
Parameters:

  • sort_particles (bool) – Makes the file reader reorder the loaded atoms before passing them to the pipeline. Sorting is based on the atom serial numbers loaded from the PDB file.

  • bounding_box (bool) – Generate an ad-hoc simulation cell as bounding box around the imported atoms.

  • centering (bool) – Translate atom coordinates and simulation box to center them at the coordinate origin.

  • generate_bonds (bool) – If true, ad-hoc bonds are created between atoms during file import based on van der Waals radii. If false, bonds are loaded from CONECT records in the input file if present.