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 T0489.a2m 1
 NameTarget T0489
// 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 T0489.try18-opt3.pdb # < try17-opt3.gromacs0 < try16-opt3 < try15-opt3 < chimera-try6-try4-try2
# ReadConformPDB T0489.try17-opt3.gromacs0.repack-nonPC.pdb # < try16-opt3 < try15-opt3 < chimera-try6-try4-try2
# ReadConformPDB T0489.try16-opt3.pdb # < try15-opt3 < chimera-try6-try4-try2
# ReadConformPDB T0489.try15-opt3.pdb # < chimera-try6-try4-try2

ReadConformPDB T0489.try6-opt3.pdb # < MQAX4-opt3.gromacs0.repack-nonPC < SAM-T08-server_TS1
# ReadConformPDB T0489.MQAX4-opt3.gromacs0.pdb # < SAM-T08-server_TS1
# ReadConformPDB T0489.MQAC1-opt3.gromacs0.pdb # < SAM-T08-server_TS1
# ReadConformPDB T0489.MQAU1-opt3.gromacs0.repack-nonPC.pdb # < SAM-T08-server_TS1


ReadConformPDB T0489.try5-opt3.gromacs0.repack-nonPC.pdb # < MQAY4-opt3 < BAKER-ROBETTA_TS2
# ReadConformPDB T0489.MQAX2-opt3.gromacs0.repack-nonPC.pdb # < BAKER-ROBETTA_TS2
# ReadConformPDB T0489.MQAY4-opt3.gromacs0.pdb # < BAKER-ROBETTA_TS2
# ReadConformPDB T0489.MQAY2-opt3.gromacs0.pdb # < Pcons_dot_net_TS3
# ReadConformPDB T0489.MQAY1-opt3.gromacs0.pdb # < Pcons_dot_net_TS3


ReadConformPDB T0489.try2-opt3.gromacs0.pdb # < try1-opt3 < align(1yqyA+2e62A)
# ReadConformPDB T0489.try1-opt3.gromacs0.pdb # < align(1yqyA+2e62A)


ReadConformPDB T0489.try4-opt3.pdb # < try3-opt3 < align(1j7nA)
# ReadConformPDB T0489.try3-opt3.gromacs0.repack-nonPC.pdb # < align(1j7nA)

# ReadConformPDB T0489.try13-opt3.pdb # chimera-N6-try6
# ReadConformPDB T0489.try12-opt3.pdb # chimera-N6-try6


InFilePrefix M1-N131/decoys/
# ReadConformPDB T0489.try4-opt3.pdb # < align(2q22A)

InFilePrefix M1-P95/decoys/
# ReadConformPDB from-M1-N131-try4.pdb # < align(2q22A)


InFilePrefix 
// ReadConformPDB T0489.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB T0489.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB T0489.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0489.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0489.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 N-join-models.pdb superpose \
	residue H89 residue E90 residue V91 residue L92 \
	residue I93 residue Y94 residue P95


printAllConformPDB C-best-models.pdb superpose \
	residue G143 residue D180 residue L194 \
	residue E219 residue F221 residue A234 \
	residue R252

# 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