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 monomeric-50pc.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

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 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 monomeric-smoothed-alpha.hist
CreateAlphaCost alpha_prev  monomeric-smoothed-alpha-1.hist -1

Time


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

InFilePrefix 

 ReadTargetSeq T0209.a2m 
 NameTarget T0209
// Now have a random conformation---use PopConform if you don't want it.
 PopConform

InFilePrefix /projects/compbio/lib/alphabet/
ReadAlphabet alpha.alphabet
InFilePrefix
CreatePredAlphaCost pred_alpha_prev alpha11 T0209.t2k.alpha.rdb 1 alpha_prev

Time

// include best previously found decoys!
InFilePrefix decoys/
OutFilePrefix decoys/


# put believed-to-be-best decoy first
ReadConformPDB T0209.try23-opt2.pdb # now the top score
ReadConformPDB T0209.try16-opt2.pdb # long-strand
ReadConformPDB T0209.try15-opt2.pdb	# mainly from robetta5
ReadConformPDB T0209.try21-opt2.pdb
ReadConformPDB T0209.try1-opt2.pdb	# full-auto


InFilePrefix 
# ReadConformPDB T0209.t2k.undertaker-align.pdb model 1
## PrintConformSheets align1.sheets
## PrintConformHelices align1.helices

Time


InFilePrefix decoys/
## ReadConformPDB robetta-model1.pdb
## PrintConformSheets robetta-model1.sheets
## ReadConformPDB robetta-model2.pdb
## PrintConformSheets robetta-model2.sheets
## ReadConformPDB robetta-model3.pdb
## PrintConformSheets robetta-model3.sheets
## ReadConformPDB robetta-model4.pdb
## PrintConformSheets robetta-model4.sheets
## ReadConformPDB robetta-model5.pdb
## PrintConformSheets robetta-model5.sheets
## PrintConformHelices robetta-model5.helices
## ReadConformPDB robetta-model6.pdb
## PrintConformSheets robetta-model6.sheets
## ReadConformPDB robetta-model7.pdb
## PrintConformSheets robetta-model7.sheets
## ReadConformPDB robetta-model8.pdb
## PrintConformSheets robetta-model8.sheets
## PrintConformHelices robetta-model8.helices
## ReadConformPDB robetta-model9.pdb
## PrintConformSheets robetta-model9.sheets
## ReadConformPDB robetta-model10.pdb
## PrintConformSheets robetta-model10.sheets


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB best-models.pdb superpose 

# Can specify a set of atoms as optional arguments of printAllConformPDB
# to give initial set of atoms to align.
# Format: 	atom A7.CA	atom K252.CA	...

Time

quit