
                        NMRPrime Strip Permutation Demo

--- scroll.com: is an example invoking the strip viewer, for adjusting
    the order of strips interactively.  In this preview version of the
    software, this general-purpose strip viewer is not directly
    connected with the tool for automated permutation.

--- To run the automated permutation demo:

    all.com

    Note that the "Draw Strips" graphics checkbox in the NMRPrime Logo 
    Window can be to toggle strip plot drawing; the assignment calculation
    will be much faster with strip drawing turned off.

--- Input Files:

hn.real.tab 

  High-quality edited HSQC peak table or equivalent.

specInfo.tab

  Lists the locations of 3D HN-detected spectra and their ordinary 
  nmrDraw peak tables for the assigment task.

seqInfo.tab

   A file with the residue sequence (in the format as used by TALOS
   et al) optionally with any prior knowledge of secondary structure that
   you might like to use.

expInfo.tab

   A file listing the types and locations of the various spectra and peak 
   tables to be used for the assignment task.  These types should correspond
   with NMRPrime's definitions of spectral types, which are recorded
   in the file "expTypes.txt"

--- Scripts:

primeImport.tcl

   Reads the tables and spectra above to create the following output files:

      join.tab    The probability that strip I is followed by strip J
                  (i.e. sequential probability).

      shifts.tab  Tentative Chemical Shift type assignments.

resProbCS.tcl

   The tentative "shifts.tab" above is used to estimate residue type
   probabilities (i.e. placement probability).  Output: resProb.tab

nmrPrime.tcl

   Permutes the order of assignments to optimize a score based on a
   weighted sum of sequential and placement probabilities.

   The results of each assignment trial are given in output: prime.tab 

