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 TR462.a2m 1
 NameTarget TR462
// 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/

ReadConformPDB TR462.try3-opt3.pdb	# < try2-opt3.gromacs0 < TR462
ReadConformPDB TR462.try2-opt3.pdb	# < TR462

ReadConformPDB TR462.pdb
#  PrintConformSheets init.sheets
#  PrintConformHelices init.helices
#     ExtractConformationsContacts 8 all_contacts rank
#     TIME
#     OptimizeConstraints all_contacts align rejected noncontact TR462.t06.CB8-sep9.rdb 
#     TIME
#     PrintContacts align		init.constraints 
#     PrintContacts rejected.bonus	init_rejected_bonus.constraints
#     PrintContacts noncontact.bonus	init_noncontact_bonus.constraints


ReadConformPDB TR462.try1-opt3.pdb	# < align(1fx7A+1r9cA+2dtr)

#ReadConformPDB from-try7-opt3.pdb

InFilePrefix 
ReadConformPDB TR462.undertaker-align.pdb model 1 # < align(2h3jA)
 PrintConformSheets align1.sheets
 PrintConformHelices align1.helices
ReadConformPDB TR462.undertaker-align.pdb model 2 # < align(2gcxA)
 PrintConformSheets align2.sheets
 PrintConformHelices align2.helices
ReadConformPDB TR462.undertaker-align.pdb model 3 # < align(1fx7A)
 PrintConformSheets align3.sheets
 PrintConformHelices align3.helices
ReadConformPDB TR462.undertaker-align.pdb model 4 # < align(1qw1A)
 PrintConformSheets align4.sheets
 PrintConformHelices align4.helices
ReadConformPDB TR462.undertaker-align.pdb model 5 3 < aligh(2dtrA)
 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