Difference between revisions of "CHARMMing's PDB Reader"

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Revision as of 17:54, 25 January 2010

CHARMMing's PDB reader exists to take a raw PDB file from the Protein Data Bank and convert it into a CHARMM-formatted PDB file. CHARMM has its own syntactic expectations for PDB files, so many PDB files will have problems when loaded into CHARMM (some of these problems are quite minor while others are potentially serious). This section of the tutorial is an explanation of how CHARMMing's PDB reader modifies a file from the PDB. It is not meant to be an exhaustive exploration of the PDB file format.

Basic algorithm

The basic algorithm used by CHARMMing is:

  1. Remove all lines that do not start with ATOM or HETATM
  2. Handle multi-model atoms. Some PDBs separate different models cleanly into different sections, but others have alternate configurations listed for individual atoms or residues within a single model

Comments

  • The PDB parser removes all lines other than ATOM and HETATM ones. A separate routine is called beforehand to parse out title, author, journal, and disulfide bond information.
  • PDBs with multiple MODEL segments are passed to a separate routine to be split into their constituent models.