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 exp-pdb.types
    ReadClashTable exp-pdb-2191-2symm.clash
    SetClashDefinition exp-pdb-2191-2symm

Time

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-2191-alpha.hist
CreateAlphaCost alpha_prev  dunbrack-2191-alpha-1.hist -1

InFilePrefix /projects/compbio/lib/alphabet/
ReadAlphabet alpha.alphabet
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 START_COL
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


# 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 real_hbond 50 real_hbond_u 50 decoy_hbond 50 decoy_hbond_u 50 \
	real_NO_hbond 10 real_NO_hbond_u 10 decoy_NO_hbond 10 decoy_NO_hbond_u 10 \
	knot 10 clens 200  rmsd 0.0 log_rmsd 35 rmsd_ca 0.0 log_rmsd_ca 30 GDT 1 smooth_GDT 1  missing_atoms 0.2

# start with no cost function
SetCost
# override the cost function here:
include COSTFCN.costfcn

Time

// read submitted models
InfilePrefix 
ReadConformPDB model1.ts-submitted
PrintConformGDT model1_domain.gdt
OutFilePrefix 
printConformPDB XXX0000_domain.model1-real.pdb superpose
OutFilePrefix decoys/
SCWRLConform
NameConform model1-scwrl

ReadConformPDB model2.ts-submitted
PrintConformGDT model2_domain.gdt
SCWRLConform
NameConform model2-scwrl

ReadConformPDB model3.ts-submitted
PrintConformGDT model3_domain.gdt
SCWRLConform
NameConform model3-scwrl

ReadConformPDB model4.ts-submitted
PrintConformGDT model4_domain.gdt
SCWRLConform
NameConform model4-scwrl

ReadConformPDB model5.ts-submitted
PrintConformGDT model5_domain.gdt
SCWRLConform
NameConform model5-scwrl

InfilePrefix decoys/
ReadConformPDB XXX0000.try1-opt2.pdb
PrintConformGDT try1_domain.gdt

OutFilePrefix 
printConformPDB XXX0000_domain.try1-real.pdb superpose
OutFilePrefix decoys/

// read models from alignment 

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

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

ReadConformPDB XXX0000.undertaker-align.pdb model 3
NameConform align3

ReadConformPDB XXX0000.undertaker-align.pdb model 4
NameConform align4

ReadConformPDB XXX0000.undertaker-align.pdb model 5
NameConform align5


InfilePrefix decoys/
include read-pdb.under

Time

OutFilePrefix decoys/
ReportCost evaluate_domain.COSTFCN.rdb
CostConform
Time

quit