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 M1-G75/decoys/
# ReadConformPDB TR462.try5-opt3.pdb

# InFilePrefix E77-V143/decoys/
# ReadConformPDB TR462.try7-opt3.pdb

InFilePrefix decoys/
ReadConformPDB TR462.try6-opt3.gromacs0.repack-nonPC.pdb	# < try5-opt3.gromacs0 < try4-opt3 < chimera-N5-C7

ReadConformPDB TR462.try8-opt3.pdb	# < try6-opt3 < try5-opt3.gromacs0 < try4-opt3 < chimera-N5-C7
ReadConformPDB TR462.try5-opt3.pdb	# < try4-opt3 < chimera-N5-C7

ReadConformPDB TR462.try4-opt3.pdb	# < chimera-N5-C7
# ReadConformPDB TR462.try4-opt3.gromacs0.repack-nonPC.pdb	# < chimera-N5-C7

# ReadConformPDB TR462.try3-opt3.gromacs0.repack-nonPC.pdb	# < chimera-N5-C7

ReadConformPDB TR462.try2-opt3.gromacs0.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
# ReadConformPDB TR462.try1-init.pdb

InFilePrefix 
// ReadConformPDB TR462.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB TR462.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB TR462.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB TR462.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB TR462.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 


printAllConformPDB C-best-models.pdb superpose \
	residue I90 residue L100 residue M103 residue L106 \
	residue  Y121 residue L130 residue Y132 \
	residue A135 residue V140

# 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