SetSeed

InfilePrefix 
// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/
ReadTrainingAtoms dunbrack-40pc-3157.atoms

# The rotamer library need not be from the same set of chains as the TrainingAtoms.
# It encodes the most probable conformations of sidechain and backbone
# for each residue type.
ReadRotamerLibrary dunbrack-40pc-3157.rot

Time


//Need to read in target before specific fragments or alignments can
// be read, also before constraints can be defined.

InFilePrefix 

# ReadTargetPDB T0473.blank.pdb
ReadTargetSeq T0473.a2m 1
NameTarget T0473
PopConform

InFilePrefix

include costfcn-init.under
# include MQA_init.costfcn
include try4.costfcn
// Scale the break and clash costs down, then gradually back up again
ScaleCost break 0.5 soft_clashes 0.



Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

InFilePrefix 
ReadTemplateAtoms Template.atoms

// try4 is intended to be a generic "polishing" script that 
//	works with existing models, rather than creating new ones from
//	alignments 

// Edit this to include full sets of alignments from any
//	strongly-predicted superfamily
// InfilePrefix 1xxxX/
//   include read-alignments-scwrl.under

Include T0473.t04.undertaker-align.under 
# TryAllAlign shrink 0 min_keep_length 1
# NameConform T0473.try4-al1


Include T0473.t06.undertaker-align.under 
# TryAllAlign shrink 0 min_keep_length 1
# NameConform T0473.try4-al1A


Include T0473.t2k.undertaker-align.under 
Include T0473.undertaker-align.under 
# TryAllAlign shrink 0 min_keep_length 1
# NameConform T0473.try4-al2

# ReadFragmentAlignment NOFILTER SCWRL force_alignment all-align.a2m
# If disulfides are expected to be important, read the aligment
# without SCWRL, since it destroys disulfides.
# Also SCWRL is *very* slow, so try to use it less on the server.
ReadFragmentAlignment NOFILTER force_alignment all-align.a2m

InfilePrefix

Time

# ReportCost try4.rdb

# TryAllAlign shrink 0. min_keep_length 1 
# NameConform T0473.try4-al3
# TryAllAlign shrink 0.2 min_keep_length 1
# NameConform T0473.try4-al4

# TryAllAlign shrink 0.3 min_keep_length 1 cumulative
# NameConform T0473.try4-al5
# TryAllAlign shrink 0.4 min_keep_length 1 
# NameConform T0473.try4-al6

# TryAllAlign shrink 0.5 min_keep_length 1 cumulative
# NameConform T0473.try4-al7
# TryAllAlign shrink 0. min_keep_length 1 
# NameConform T0473.try4-al8

# SCWRLConform
# NameConform T0473.try4
OutFilePrefix decoys/
# PrintConformPDB T0473.try4-init.pdb


// Switch to the following (commenting out the TryAllAlign)
// to polish existing models
InfilePrefix decoys/
 include read-pdb.under


ReportCost debug.rdb

CostConform
Time