# YASARA MACRO
# TOPIC:       5. Structure prediction
# TITLE:       Building a homology model
# REQUIRES:    Structure
# AUTHOR:      Elmar Krieger
# LICENSE:     GPL
# DESCRIPTION: This builds a homology model using a FASTA sequence of the target, and optionally template structures and alignments

# Parameter section - adjust as needed
# ====================================

# You can either set the target structure by clicking on Options > Macro > Set target,
# or by uncommenting the line below and specifying it directly.
#MacroTarget='/home/myname/projects/homologymodels/t0120'

# Number of PSI-BLAST iterations
psiblasts = 6

# Maximum PSI-BLAST Evalue allowed for templates
evalue = 0.5 

# Maximum number of PDB templates to use
templates = 5

# Maximum number of ambiguous alignments to consider per template
alignments = 5

# Maximum oligomerization state, build at most dimeric models
oligostate = 2

# Normally no change required below this point

# Sanity checks
if MacroTarget==''
  RaiseError "This macro requires a target. Either edit the macro file or click Options > Macro > Set target to choose a target sequence"

Clear

# Do we have a target sequence? 
command1='pass'
seqfilename='(MacroTarget).fasta'
seq = FileSize (seqfilename) 
if seq
  # Yes, create a command to specify the sequence file
  command1='SequenceFile (seqfilename)'
  
# Do we have alignments?
alifilename='(MacroTarget)_align.fasta'
ali = FileSize (alifilename) 
if ali
  # Yes, use the alignments instead of the target sequence
  command1='AlignFile (alifilename)'
  
# Do we have templates?
command2='pass'
for i=001 to 999
  for ext in 'pdb','yob'
    tmpfilename='(MacroTarget)_t(i).(ext)'
    tmp = FileSize (tmpfilename)
    if tmp
      # Load template and name it T001.. 
      tmp = Load(ext) (tmpfilename)
      NameObj (tmp),T(i)
      # Create command to select all templates
      command2='TemplateObj all'
      # Template found, try next
      continue 2
  break

# Build the model
Experiment HomologyModeling
  # Specify either a target sequence or an alignment file
  (command1)
  # Specify any templates that have been loaded
  (command2)
  # Set parameters defined at the beginning
  # Number of PSI-BLAST iterations
  PsiBLASTs (psiblasts)
  # The maximum PSI-BLAST Evalue (minimum can be set to avoid easy models)
  EValue Max=(evalue),Min=0
  # Maximum oligomerization state
  OligoState (oligostate)
  # Maximum number of templates to consider, and how many with the same sequence
  Templates (templates),SameSeq=1
  # Maximum number of ambiguous alignments to consider per template
  Alignments (alignments)
  # And some less important parameters
  # Speed of animations: fast/normal/slow
  Animation Normal
  # Number of samples to try per loop (see OptimizeLoop command)
  LoopSamples 50
  # The common start for result filenames
  ResultFile (MacroTarget)
Experiment On
Wait ExpEnd

# Tell about the homology modeling report
ShowMessage 'To view a detailed homology modeling report, open (MacroTarget).html in your browser.'
Wait ContinueButton 
HideMessage