Example of structure determination of Ail using the implicit solvent force 
field EEFx with implicit membrane.

          F.M. Marassi, Yi Ding, C.D. Schwieters, Ye Tian and Yong
          Yao, ``Backbone structure of Yersinia pestis Ail determined
          in micelles by NMR-restrained simulated annealing with
          implicit membrane solvation,'' J. Biomol. NMR 63, 59-65
          (2015). 


0) EEFx-membrane reference:

  jBiomolNMR63_59_2015.pdf

1) Calculate structure from random coordinates

  % xplor -py fold_EFF.py

  (results are in precalc/fold_EEF*)

2) create files with suffix .best for 10 lowest energy structures

  % getBest -symlinks -num 10 fold_EFF_##.sa.stats 

  (results are in precalc/refine_EEF*)

3)  Refinement of ten best structures from the fold calculation

  % xplor -py -parallel refine_EEF.py 

4) The resulting lowest 10 energy structures should have accuracy to the
   reference structures of less than 1.3 angstroms as determined by

  % targetRMSD -selection "name CA and (resid 29:41 or resid 53:62 or resid 67:77 \
                    or resid 94:106 or resid 111:124 or resid 136:152 \
		     or resid 155:165 or resid 170:181)" -diffSeq 3qra.pdb \
          -selection2 "name CA and (resid 3:15 or resid 27:36 or resid 41:51 or \
	  	   resid 68:80 or resid 85:98 or resid 110:126 or resid 129:139 \
		   or resid 144:155)" \
          `getBest -num 10 refine_EEF_##.sa.stats `

5) Folding and refinement with REPEL (the default repulsive-only
   nonbonded term) only with fold_EEF.py and refine_EEF.py,
   respectively. Compare the RMSD determined with this term:

  % targetRMSD -selection "name CA and (resid 29:41 or resid 53:62 or resid 67:77 \
                    or resid 94:106 or resid 111:124 or resid 136:152 \
		     or resid 155:165 or resid 170:181)" -diffSeq 3qra.pdb \
          -selection2 "name CA and (resid 3:15 or resid 27:36 or resid 41:51 or \
	  	   resid 68:80 or resid 85:98 or resid 110:126 or resid 129:139 \
		   or resid 144:155)" \
          `getBest -num 10 refine_REPEL_##.sa.stats `
