model.write_pdb_xref() -- write residue number/index correspondence

aln = <alignment>		Alignment between model and templates
file = <str:1>	'default'	partial or complete filename
output_directory = <str:1>	''	output directory
model_segment = <str:2>	'FIRST:@' 'LAST:'	segment to be read in

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: examples/commands/write_pdb_xref.py

# Example for: model.write_pdb_xref()

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

log.verbose()
env = environ()

mdl = model(env, file='2abx.atm', model_segment=('FIRST:@', 'END:'))
aln = alignment(env)
aln.append_model(mdl, align_codes='2abx')

# if not found, 1, NRES used
mdl.write_pdb_xref(aln, file='2abx.xref1', model_segment=('FIRST:@', 'END:'))

# You can use string resid's
mdl.write_pdb_xref(aln, file='2abx.xref2', model_segment=('1:', '50:'))

# You can use integer resid's
mdl.write_pdb_xref(aln, file='2abx.xref3', model_segment=('!2', '!50'))

# You can even use the alignment specs, but not with codes that start with '!'
mdl.write_pdb_xref(aln, file='2abx.xref4', model_segment=('2abx', '2abx'))

# You can mix the specs
mdl.write_pdb_xref(aln, file='2abx.xref5', model_segment=('!2', '50:'))
mdl.write_pdb_xref(aln, file='2abx.xref6', model_segment=('!2', 'END:'))