PDB info files are designed to address the need for easy access to a subset of the information in a PDB files. They contain selected per-residue information in a easier to use form as well as an alignment of the SEQRES-defined and ATOM-defined residues produced with SAM.
A PDB info file is created per-chain in RDB format and named in the form
1abcD.pdb-rdb.gz. The
pdb-get-info command is used
to access the files, creating them in a lazy manner. It also allows
for transparently creating files from MAXSPOUT and hand-modified PDB files.
The comment section at the top of the RDB file contains chain global information, stored as variables in the form:
# name=value
The following variables are currently defined:
pdbId - PDB Id of the chain (includes chain), e.g.: 1burA
pdbCode - PDB code of the protein (no chain), e.g.: 1bur
chain - Chain identifier, or empty if none.
pdbFile - Path to the PDB file that was used to create the this file.
numResidues - Number of residues in file.
numInserts - Number of SEQRES insert residues in file.
noteN - Textual note messages.
warningN - Textual warning messages.
pdbToolsVersion - Version of PDB tools used to create
this file.
The rows in RDB file contain residue information. This contains all
residues upto the TER record, include HETATMs
with full backbones. The following columns are defined:
POS - Sequential, one based position number.
SEQNUM - If the residue is defined in the ATOM,
records, this is the residue sequence number, including insert code.
If the residues is a SEQRES insert, this column is blank.
AA3 - The three-letter amino acid or heterogen code.
If this is a SEQRES insert, it is lower-case.
AA - One letter amino acid code. If this is a
SEQRES insert, it is lower-case.
For modified residues, the letter is mapped to the unmodified residue
letter.