WRITE_PDB_XREF -- write residue topology library

FILE = $\langle{\tt string:1}\rangle$	'default'	partial or complete filename
OUTPUT_DIRECTORY = $\langle{\tt string:1}\rangle$	''	output directory
MODEL_SEGMENT = $\langle{\tt string:2}\rangle$	'FIRST:@' 'LAST:'	segment to be read in
ALIGN_CODES = $\langle{\tt string:0}\rangle$	'all'	codes of proteins in the alignment
ATOM_FILES = $\langle{\tt string:0}\rangle$	''	complete or partial atom filenames

Description:

This command writes the correspondence between the PDB residue numbers and residue indices for the selected part of the MODEL. It is more useful than one would think because of its interaction with the alignment data and the option to use wild characters to specify the beginning and ending residues.

Example:

# Example for: WRITE_PDB_XREF

# This writes out information useful for relating PDB residue numbers with
# residue indices.

SET OUTPUT_CONTROL = 1 1 1 1 1

READ_MODEL FILE = '2abx.atm', MODEL_SEGMENT = 'FIRST:@' 'END:'
SEQUENCE_TO_ALI ALIGN_CODES = '2abx'

WRITE_PDB_XREF FILE = '2abx.xref1',MODEL_SEGMENT='FIRST:@'  'END:'  # if not found, 1, NRES used
WRITE_PDB_XREF FILE = '2abx.xref2',MODEL_SEGMENT='1:'   '50:'  # You can use string resid's
WRITE_PDB_XREF FILE = '2abx.xref3',MODEL_SEGMENT='!2'  '!50'   # You can use integer resid's
WRITE_PDB_XREF FILE = '2abx.xref4',MODEL_SEGMENT='2abx' '2abx' # You can even use the alignment 
                                                               # specs, but not with ALIGN_CODES 
                                                               # that start with '!'
WRITE_PDB_XREF FILE = '2abx.xref5',MODEL_SEGMENT='!2'   '50:'  # You can mix the specs
WRITE_PDB_XREF FILE = '2abx.xref6',MODEL_SEGMENT='!2'  'END:'  # You can mix the specs