XPDB (Extended PDB file)¶

Coordinate reader	`MDAnalysis.coordinates.PDB.ExtendedPDBReader`
Topology parser	`MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser`

The extended PDB reader acts virtually the same as the PDB, ENT (Standard PDB file) reader. The difference is that extended PDB files (MDAnalysis format specifier XPDB) may contain residue sequence numbers up to 99,999 by utilizing the insertion character field of the PDB standard. Five-digit residue numbers may take up columns 23 to 27 (inclusive) instead of being confined to 23-26 (with column 27 being reserved for the insertion code in the PDB standard).

PDB files in this format are written by popular programs such as VMD.

As extended PDB files are very similar to PDB files, tell MDAnalysis to use the Extended PDB parser by passing in the topology_format keyword.

In [1]: import MDAnalysis as mda

In [2]: from MDAnalysis.tests.datafiles import PDB

In [3]: pdb = mda.Universe(PDB)

In [4]: pdb.trajectory.format
Out[4]: ['PDB', 'ENT']

In [5]: xpdb = mda.Universe(PDB, topology_format='XPDB')

In [6]: xpdb.trajectory.format
Out[6]: 'XPDB'