
Example of paramagnetic relaxation enhancement used for refining a
protein-DNA complex.  

  Reference: 
  
    J. Iwahara, C.D. Schwieters, and G.M. Clore, ``Ensemble approach for
    NMR structure refinement against 1H paramagnetic relaxation
    enhancement data arising from a flexible paramagnetic group attached
    to a macromolecule,'' J. Am. Chem. Soc. 126, 5879-5896 (2004) 


1) Generate a PSF file of the SRY/DNA complex including
   paramagnetic tags on three locations of the DNA. Three copies of
   each tag are made such that the distribution of the floppy tag
   coordinates can be represented. Coordinates are read in from a
   starting pdb (1J46), all atoms with unknown coordinates are given
   proper coordinates, and the pdb is written out.

  % xplor -py generate.py

  [This creates the files generate.psf and generate.pdb.]

2) Compare starting, reference structures:

  % vmd-xplor 1j46.pdb -psf generate.psf generate.pdb

2) Refine the starting structure using PREs, NOEs, RDCs, 13C
   chemical shifts, J-couplings, and dihedral angle restraints.

 % xplor -py refine.py

  [One structure takes <25 min on contemporary CPUs.]

3) Validation of the results show that the structures don't quite have
   the quality of the published results. This DNA construct has
   additional base pairs beyond the input structure, such that an
   additional refinement run is necessary to get the published
   results.

 % xplor -py validate.py

  [ Validation errors appear at the end of this script. ]

4) Use the lowest energy structure of refine.py as the starting
   coordinates of a second refinement calculation.

 % cp `getBest -num 1 validate_##.pdb.stats` start.pdb
 % xplor -py refine2.py

5) Validation of these structures should succeed.

 % xplor -py validate2.py


Files:

  refStruct.pdb   - reference structure of the complex
  inputs/         - directory containing various input tables, parameters, etc.

