# YASARA MACRO
# TOPIC:       5. Structure Determination
# TITLE:       Solve an NMR structure with fixed quality
# REQUIRES:    YASARA Structure and NMR Structure Determination Module
# AUTHOR:      Elmar Krieger, Sander Nabuurs, Chris Spronk
# LICENSE:     GPL
# DESCRIPTION: This macro solves an NMR structure based on a protein sequence and a restraint file in XPLOR format. Contrary to the normal nmr_solve macro, it refines only those structures in water, that match a quality criterion, and performs an unlimited number of folding runs until the ensemble has the requested size

# To solve a structure with fixed quality, you need:
# - The protein sequence, in FASTA or PDB format,
#   default filenames are 'sequence.pdb' or 'sequence.fasta'
# - A file with distance and dihedral angle restraints,
#   default filename is 'restraints.tbl'
#
# You can either set the target by clicking on Options > Macro > Set target,
# by providing it as command line argument (see docs at Essentials > The command line),
# or by uncommenting the line below and specifying it directly.
#macrotarget = 'c:\MyProject\1crn'

# If you want to change the defaults, do it here
# (look in nmr_setdefaults to see what you can change)

# Number of structures in the ensemble
ensemblesize=10

# Fold the structure from the stretched out conformation
structures=ensemblesize
include nmr_fold

# Continue indefinitely until we have enough structures
try=1
current=001
defaultscalebak()=defaultscale
while current<=ensemblesize
  # Fold only one structure at a time
  start=current
  structures=1
  # To avoid infinite loops, we slightly increase the scaling factors with every try
  # (and most importantly, this also makes sure that every structure is different)
  defaultscale=defaultscalebak+0.1*try
  # Create something that looks like a real protein by in vacuo refinement
  include nmr_refinevacuo
  # Load the best structure from in vacuo refinement
  Clear
  LoadPDB (ensemblefile)(current)
  Load(restrainformat) (restrainfile),1,NameFormat=(nameformat)
  # See if it's acceptable, 
  dissum,dismax,dihsum,dihmax,rdcsum,rdcmax = RestViol
  if dismax<violdismax and dihmax<violdismax and rdcmax<violrdcmax
    # Structure is acceptable
    LogAs (logfile),append=yes,print 'Try (try): Quality conditions satisfied, accepted as structure (current) in the ensemble.'
    current=current+1
  else
    LogAs (logfile),append=yes,print 'Try (try): Quality conditions violated, dismax=(0.0+dismax), dihmax=(0.0+dihmax), trying again...'
  try=try+1

# Use everything we got to arrive at an accurate structure by explicit solvent refinement
structures=ensemblesize
start=001
include nmr_refinesolvent

# Analyze the quality and create the final bundle
include nmr_analyze
  
# Exit YASARA if this macro was provided as command line argument in console mode and not included from another macro
if runWithMacro and ConsoleMode and !IndentationLevel
  Exit