SetSeed

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

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 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 dunbrack-1332-alpha.hist
CreateAlphaCost alpha_prev  dunbrack-1332-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 T0240.a2m
ReadTargetPDB ../T0240.blank.pdb	# get from monomer
NameTarget T0240
// Now have a random conformation---use PopConform if you don't want it.

PopConform // get rid of random conformation

Time

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

include ../unconstrained.costfcn

Time

MakeGenericFragmentLibrary
Time


InFilePrefix 
ReadFragmentAlignment ../1ihrA/T0240-1ihrA-t2k-local-str2+CB_burial_14_7-0.4+0.4-adpstyle5.a2m NOFILTER SCWRL

TryAllAlign shrink 0 min_keep_length 1
NameConform T0240-1ihrA-crude-monomer
PrintConformPDB T0240-1ihrA-crude-monomer.pdb



quit