SetSeed


// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
 InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/
ReadTrainingAtoms monomeric-50pc.atoms
ReadRotamerLibrary dunbrack-1332.rot

InFilePrefix /projects/compbio/experiments/undertaker/spots/
#    ReadAtomType pdb-name.types
#    ReadClashTable pdb-1332-2symm.clash
#    SetClashDefinition pdb-2symm
    ReadAtomType exp-pdb.types
    ReadClashTable exp-pdb-1332-2symm.clash
    SetClashDefinition exp-pdb-2symm

Time


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

InFilePrefix 

 ReadTargetPDB XXX0000.blank.pdb
# ReadTargetSeq XXX0000.a2m
NameTarget XXX0000
PopConform

# Read real conformation

# Read conformation by specifying a PDB id
clearIDs 
AddID REAL_PDB

# DO READ
# ReadConformPDBids
# ReadConformPDB XXX0000_domain.real.pdb

SaveConformAsReal

OutFilePrefix decoys/
# PrintConformGDT real-vs-real.gdt
# quit

## SetRealCost rmsd 0.0 rmsd_ca 0.0 missing_atoms 0.0 GDT 0.0 smooth_GDT 1.0
## CreateBurialCost dry5 monomeric-50pc-dry-5.spot smoothed-monomeric-50pc-dry-5.hist
## CreateBurialCost wet6.5 monomeric-50pc-wet-6.5.spot smoothed-monomeric-50pc-wet-6.5.hist log
## CreateBurialCost dry6.5 monomeric-50pc-dry-6.5.spot smoothed-monomeric-50pc-dry-6.5.hist
## CreateBurialCost gen6.5 monomeric-50pc-generic-6.5.spot smoothed-monomeric-50pc-generic-6.5.hist
## CreateBurialCost near_backbone near-backbone-center.spot smoothed-near-backbone-2spot.hist near-backbone-count.spot
## CreateBurialCost way_back way-back-center.spot smoothed-way-back-2spot.hist way-back-count.spot
## CreateBurialCost dry8 monomeric-50pc-dry-8.spot smoothed-monomeric-50pc-dry-8.hist
## CreateBurialCost dry10 monomeric-50pc-dry-10.spot smoothed-monomeric-50pc-dry-10.hist
## CreateBurialCost dry12 monomeric-50pc-dry-12.spot smoothed-monomeric-50pc-dry-12.hist
## CreateAlphaCost alpha dunbrack-1332-alpha.hist
## CreateAlphaCost alpha_prev  dunbrack-1332-alpha-1.hist -1
## 
## InFilePrefix /projects/compbio/lib/alphabet/
## ReadAlphabet alpha.alphabet
## Time
## 
## InFilePrefix
## include try1.costfcn

# perfect match should be cost -1.
# different components are scaled to have roughly equal weight
# (roughly a difference of 1 between great models and totally wrong ones)
SetRealCost knot 0.1 clens 0.5  rmsd 0.0 log_rmsd 0.13 rmsd_ca 0.0 log_rmsd_ca 0.13 GDT 0.005 smooth_GDT 0.005
SetCost missing_atoms 0

Time

// read models from alignment 

InFilePrefix
ReadConformPDB XXX0000.t2k.undertaker-align.pdb model 1
NameConform align1
PrintConformGDT align1_domain.gdt

ReadConformPDB XXX0000.t2k.undertaker-align.pdb model 2
NameConform align2
PrintConformGDT align2_domain.gdt

ReadConformPDB XXX0000.t2k.undertaker-align.pdb model 3
NameConform align3
PrintConformGDT align3_domain.gdt


// read submitted models
InfilePrefix
ReadConformPDB model1.ts-submitted
PrintConformGDT model1_domain.gdt

OutFilePrefix 
printConformPDB XXX0000_domain.model1-real.pdb superpose
OutFilePrefix decoys/

ReadConformPDB model2.ts-submitted
PrintConformGDT model2_domain.gdt
ReadConformPDB model3.ts-submitted
PrintConformGDT model3_domain.gdt
ReadConformPDB model4.ts-submitted
PrintConformGDT model4_domain.gdt
ReadConformPDB model5.ts-submitted
PrintConformGDT model5_domain.gdt

InFilePrefix decoys/

ReadConformPDB XXX0000.try1-opt2.pdb
PrintConformGDT try1-opt2_domain.gdt
PopConform

include read-pdb.under

Time

OutFilePrefix decoys/
ReportCost evaluate_domain.rdb
CostConform
Time

ReadConformPDB robetta-model1.pdb
PrintConformGDT robetta1_domain.gdt
Popconform

ReadConformPDB robetta-model2.pdb
PrintConformGDT robetta2_domain.gdt
Popconform

ReadConformPDB robetta-model3.pdb
PrintConformGDT robetta3_domain.gdt
Popconform

ReadConformPDB robetta-model4.pdb
PrintConformGDT robetta4_domain.gdt
Popconform

ReadConformPDB robetta-model5.pdb
PrintConformGDT robetta5_domain.gdt
Popconform

Time
quit