Icon  Name                    Last modified      
[TXT] 0README.txt 2018-03-12 15:58 [   ] bicelles_hnc.tbl 2017-05-03 16:17 [   ] bicelles_nc.tbl 2017-05-03 16:17 [   ] bicelles_nh.tbl 2017-05-03 16:17 [   ] chapter.pdf 2017-12-15 16:58 [   ] dihedral.tbl 2017-05-03 16:17 [TXT] fold.py 2017-05-03 16:17 [   ] gb1.seq 2017-05-03 16:17 [   ] methodsMolBiol.tar.gz 2017-05-22 10:23 [   ] noe.tbl 2017-05-03 16:17 [TXT] refine.py 2017-05-03 16:17 [   ] tmv107_hnc.tbl 2017-05-03 16:17 [   ] tmv107_nc.tbl 2017-05-03 16:17 [   ] tmv107_nh.tbl 2017-05-03 16:17

Example of molecular dynamics/simulated anneanling structure determination using 
distance, torsion angle, and bond-vector orientation (from RDCs) restraints, as 
described in detail in:

  C.D. Schwieters, G.A. Bermejo, ``Protein Structure Elucidation from NMR
  Data with the Program Xplor-NIH,'' Methods Mol Biol. 1688, 311-340 (2018).

[available here as chapter.pdf]

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Run the following programs (in the order in which they appear):

# Generate a PSF file from sequence.
seq2psf gb1.seq

# Calculate a set of structures starting from extended conformations.
xplor -py fold.py > fold.log


# Return a symbolic link to the top-scoring structure calculated by fold.py.
getBest -num 1 -symlinks


# Calculate a set of structures by refining the top-scoring one from fold.py.
xplor -py refine.py > refine.log

  [ Running these commands requires that the Xplor-NIH helper programs
  are in your PATH. This can be accomplished by adding the bin
  directory of the Xplor-NIH distribution to your PATH, or using the
  -symlinks option to ./configure so that the commands are available
  from a directory already in your PATH. ]


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fold.py is exactly as presented in the reference, except for the following changes:

* The nstructures variable has been added at the very beginning to specify the
  wanted number of structures.