COORD_FORMAT (CCP4: Supported Program)

NAME

coord_format - fix PDB format and convert to/from other formats

SYNOPSIS

coord_format xyzin foo_in.xyz xyzout foo_out.xyz
[Key-worded input file]

DESCRIPTION

coord_format has two purposes:
  1. Syntax checking on input is less strict than other programs. Therefore, a corrupted PDB file can be read in, and output as a "standardised" PDB file. It is the user's responsibility to check that the program has interpreted the input correctly.
  2. The program will convert between PDB, mmCIF and MMDB binary formats. Because of the limitations of the various formats, this conversion is not exact, and again the user should check the output carefully.

INPUT AND OUTPUT FILES

XYZIN

Input coordinate file. The input format is detected automatically.

XYZOUT

Output coordinate file, in format selected by OUTPUT keyword.

KEYWORDED INPUT

OUTPUT [ PDB | CIF | BIN ]

(default is PDB)
Select output file format: PDB = standard PDB format, CIF = mmCIF format, and BIN = MMDB binary format.

FIXBLANK

Fix files with a missing or blank chain ID. For example, it is quite common to find that files in the PDB archive which contain a single protein chain do not have a chain ID set. If this option is set, the program will assign affected residues to the next available chain ID. If there appears to be more than one chain involved (e.g. both protein and waters have a blank chain ID), then more than one chain ID will be created.

If all residues in a file have an associated chain ID, then this option will have no effect, i.e. it is safe to use.

END

End keyworded input.

PROGRAM OUTPUT

The program currently gives a short summary of the commands received.

AUTHORS

Eugene Krissinel, European Bioinformatics Institute, Cambridge, UK.
Martyn Winn, Daresbury Laboratory, UK