# YASARA MACRO
# TOPIC:       5. Structure Determination
# TITLE:       Set default parameters for NMR structure determination
# REQUIRES:    YASARA Structure and NMR Structure Determination Module
# AUTHOR:      Elmar Krieger, Sander Nabuurs, Chris Spronk
# LICENSE:     GPL
# DESCRIPTION: This macro is included by others to set default parameters

# If you make changes here, they will globally affect all NMR macros.
# The 'count' function is used to make sure that none of the local
# settings you made before are overwritten here.

if not count seqfile
  # The sequence filename (can have either .fasta or .pdb extension)
  # If a PDB file is given, it must contain a SEQRES record
  seqfile='sequence'
  
if not count restfile
  # The restraint filename (normally .tbl extension)
  restrainfile='restraints'

if not count ensemblefile
  # The ensemble filename
  ensemblefile='ensemble'

if not count structures
  # The number of structures to generate
  structures=10

if not count ph
  # The pH at which the NMR spectrum was recorded.
  # (This information will be used in the final explicit solvent refinement step
  #  to assign protonation states of Asp, Glu and His residues).
  ph=7.0

if not count defaultpot
  # The normal restraining function (see RestrainPot command)
  defaultpot='SoftSquare, SqConstant=1.00, SqOffset=0.0, SqExponent=2, rSwitch=1.00, SoExponent=1, Asymptote=2.00'

if not count defaultpar 
  # The normal restraining parameters (see RestrainPar command)
  defaultpar='Average=Sum, Ceil=9999, Monomers=1, JoinDis=-1'
  
if not count defaultscale 
  # The normal scaling factors for restraints
  defaultscale='Distance=25, Dihedral=2'

if not count strongscale 
  # The strong scaling factors for restraints
  strongscale='Distance=50, Dihedral=5'
    
if not count violdismax
  # The maximum allowed distance restraint violation in A, 9999 to ignore
  violdismax=0.5
  
if not count violdihmax
  # The maximum allowed dihedral angle restraint violation in degrees, 9999 to ignore
  violdihmax=5

if not count correctcispro
  # Flag if cis-peptide bonds before prolines should be corrected.
  # If you do not want to potentially miss a cis-proline in your structure,
  # set this flag to 'No'. If the lowest energy structures in the ensemble
  # then all have a certain cis-proline, fix it in the cis-conformation.
  # In any case, create a new ensemble with the flag set to 'Yes' to avoid
  # a random collection of cis-prolines.
  correctcispro='Yes'

if not count cysbridgelist
  # Treatment of cysteine bridges:
  # Option 1: Assign them automatically, bridge cysteines close in space
  cysbridgelist()='Auto'
  # Option 2: Explicity link the specified pairs of cysteine residues (example 1CRN)
  #cysbridgelist()=3,40, 4,32, 16,26
  # Option 3: Don't form cysteine bridges
  #cysbridgelist()='None'
  
if not count floating
  # Floating assignment
  # Option 1: No floating assignments
  floating='None'  
  # Option 2: All hydrogens 
  # floating='Element H'
  
if not count fofwater
  # The force field used for simulations in explicit solvent
  fofwater='Yasara'

if not count fofscale
  # Scaling factor for the force field energy when sorting the final ensemble
  # (due to electrostatics and solvation, force field energies are on a larger
  #  scale than restraint violation energies. If they were not scaled down, even
  #  structures with large restraint violations could be ranked first if they
  #  had excellent electrostatics).
  fofscale=0.1
  
if not count logfile
  # The log filename
  logfile='result'

# No changes required below  
  
if not count start
  # The number of the structure to start with
  start=001
 
if count MacroTarget and MacroTarget!=''
  # A target directory has been defined, go there
  MacroTarget = dirname MacroTarget
  CD (MacroTarget)