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-2191.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 

 ReadTargetSeq T0487.a2m 173
 NameTarget T0487
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/


# put believed-to-be-best decoy first
InFilePrefix decoys/
// include read-pdb.under

ReadConformPDB T0487.try13-opt3.pdb	# < try11-opt3.gromacs0 < from-try3

ReadConformPDB from-try3.pdb
# PrintConformSheets from-try3.sheets
# PrintConformHelices from-try3.helices
ReadConformPDB T0487.try10-opt3.pdb # < align(2b82A+1jiwI+1ofuX+1fjgT+1s3jA)


ReadConformPDB T0487.try7-opt3.gromacs0.pdb # < align(2b82A+1rmwA+2ethA+3bjaA+2b82A)
ReadConformPDB T0487.try9-opt3.pdb # < align(1rmwA+2gqcA+1s3jA+1oftA+1ev7A)
ReadConformPDB T0487.try8-opt3.pdb # < align(2b82A+2vqeT+1smpI+3bj6A+1rmwA+1s3jA)


ReadConformPDB	T0487.try5-opt3.repack-nonPC.pdb # < align(1rmwA+1xd5A+2gqcA+1nhpA+1jiwI+3bj6A+1jiwI)

ReadConformPDB from-MQAU1.pdb
# PrintConformSheets from-MQAU1.sheets
# PrintConformHelices from-MQAU1.helices

ReadConformPDB	T0487.try4-opt3.pdb # < align(2b82A+1jiwI+1rmwA+1iow+1ev7A+1iow)

ReadConformPDB	T0487.try2-opt3.pdb # < try3-opt3 < align(2b82A+2gqcA+2vqeT+2hwkA+1xd5A)
# ReadConformPDB	T0487.try3-opt3.pdb # < align(2b82A+2gqcA+2vqeT+2hwkA+1xd5A)

ReadConformPDB from-try5.pdb
# PrintConformSheets from-try5.sheets
# PrintConformHelices from-try5.helices

ReadConformPDB T0487.try1-opt3.pdb



InFilePrefix 
ReadConformPDB T0487.undertaker-align.pdb model 5	(1u04A)
 PrintConformSheets align5.sheets
 PrintConformHelices align5.helices

#ReadConformPDB T0487.undertaker-align.pdb model 8	(1jiwI)
# PrintConformSheets align8.sheets
# PrintConformHelices align8.helices


// ReadConformPDB T0487.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB T0487.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB T0487.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0487.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0487.undertaker-align.pdb model 5
# PrintConformSheets align5.sheets
# PrintConformHelices align5.helices

Time


// 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