PDB_TO_XYZ
Write PDB Atom Coordinates to XYZ File

PDB_TO_XYZ is a FORTRAN90 program which reads a PDB file, and, for each ATOM record in the file, extracts the atomic spatial coordinates and writes them to an XYZ file.

Usage:

pdb_to_xyz

starts the program, and prompts for the file names.

pdb_to_xyz file.pdb file.xyz

starts the program, reads the data from file.pdb, and creates file.xyz.

Licensing:

The computer code and data files described and made available on this web page are distributed under the GNU LGPL license.

Languages:

PDB_TO_XYZ is available in a FORTRAN90 version.

Related Data and Programs:

PDB, a data directory which contains a description and examples of the PDB format.

PDB_EXTRACT, a FORTRAN90 program which can extract certain records from a PDB file.

PDB_READ, a FORTRAN90 program which can read the information in a PDB file.

XYZ, a data directory which contains a description and examples of the XYZ format.

XYZ_IO, a FORTRAN90 library which reads and writes XYZ files.

XYZ_TO_PDB, a FORTRAN90 program which reads a set of XYZ spatial coordinates, and rewrites them as ATOM records in a PDB file.

Reference:

1. http://www.rcsb.org/pdb/
   The Protein Data Bank Home Page.

Source Code:

• pdb_to_xyz.f90, the source code;
• pdb_to_xyz.csh, commands to compile the source code;

Examples and Tests:

TINY is a sample PDB file with 12 atoms.

• tiny.pdb, a sample PDB file;
• tiny.xyz, the corresponding XYZ file.

MONOMER is a sample PDB file with 888 atoms.

• monomer.pdb, a sample PDB file;
• monomer.xyz, the corresponding XYZ file.

List of Routines:

• MAIN is the main program for PDB_TO_XYZ.
• CH_CAP capitalizes a single character.
• GET_UNIT returns a free FORTRAN unit number.
• PDB_ATOM_TO_XYZ reads the ATOM records in a PDB file.
• S_EQI is a case insensitive comparison of two strings for equality.
• TIMESTAMP prints the current YMDHMS date as a time stamp.

You can go up one level to the FORTRAN90 source codes.