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 T0296.blank.pdb
ReadTargetSeq T0296.a2m 1
NameTarget T0296
PopConform

# Read real conformation

# Read conformation by specifying a PDB id
clearIDs 
AddID 2ha9A

# DO READ
ReadConformPDBids
# ReadConformPDB T0296.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 140 knot 1000 clens 100  rmsd 0.0 log_rmsd 35 rmsd_ca 0.0 log_rmsd_ca 30 GDT 1 smooth_GDT 1  missing_atoms 0.1

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

Time

// read submitted models
InfilePrefix 
ReadConformPDB model1.ts-submitted
PrintConformGDT model1.gdt
SCWRLConform
NameConform model1-scwrl


OutFilePrefix 
printConformPDB T0296.model1-real.pdb superpose
OutFilePrefix decoys/


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

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

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

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

InfilePrefix decoys/
ReadConformPDB T0296.try1-opt2.pdb
PrintConformGDT try1.gdt

OutFilePrefix 
printConformPDB T0296.try1-real.pdb superpose
OutFilePrefix decoys/

// read models from alignment 

InFilePrefix
ReadConformPDB T0296.undertaker-align.pdb model 1
NameConform align1
PrintConformGDT align1.gdt

ReadConformPDB T0296.undertaker-align.pdb model 2
NameConform align2
PrintConformGDT align2.gdt

ReadConformPDB T0296.undertaker-align.pdb model 3
NameConform align3

ReadConformPDB T0296.undertaker-align.pdb model 4
NameConform align4

ReadConformPDB T0296.undertaker-align.pdb model 5
NameConform align5


InfilePrefix decoys/
include read-pdb+servers.under

Time

OutFilePrefix decoys/
ReportCost evaluate.unconstrained.rdb
CostConform
Time

quit