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

//Need to read in target before specific fragments or alignments can
// be read, also before constraints can be defined.
InFilePrefix /projects/compbio/experiments/protein-predict/casp8/T0514/decoys/SAM_T08//

# ReadTargetPDB T0514.blank.pdb
ReadTargetSeq T0514.a2m 1
NameTarget T0514
PopConform

# Read real conformation

# Read conformation by specifying a PDB id
clearIDs 
AddID 3dtdA

# DO READ
ReadConformPDB	T0514_D1.pdb
NameConform	T0514_D1
# 

SaveConformAsReal

OutFilePrefix D1/decoys/
# 
# 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)
# Mon Feb  9 13:36:31 PST 2009 John Archie: changed real_cost to published version
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 0 clens 200  rmsd 0.0 log_rmsd 35 rmsd_ca 0.0 log_rmsd_ca 30 GDT 1 smooth_GDT 1  missing_atoms 0

include costfcn-init-eval.under
# start with no cost function
SetCost
# override the cost function here:


Time

// read submitted models
InfilePrefix /projects/compbio/experiments/protein-predict/casp8/T0514/decoys/SAM_T08//


OutFilePrefix 

OutFilePrefix D1/decoys/























InfilePrefix /projects/compbio/experiments/protein-predict/casp8/T0514/decoys/SAM_T08//decoys/



OutFilePrefix 

OutFilePrefix D1/decoys/

// read models from alignment 

InFilePrefix /projects/compbio/experiments/protein-predict/casp8/T0514/decoys/SAM_T08//


















InfilePrefix decoys/
include read-servers.under

Time

OutFilePrefix D1/decoys/
ReportCost servers-real_cost.rdb
CostConform
Time

quit