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 T0335.a2m 1
 NameTarget T0335
// 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-H77/decoys/
ReadConformPDB T0335.try8-opt2.pdb
# ReadConformPDB T0335.try6-opt2.pdb
# ReadConformPDB T0335.try2-opt2.pdb


InFilePrefix decoys/
ReadConformPDB T0335.try9-opt2.pdb
#ReadConformPDB T0335.try13-opt2.pdb
#ReadConformPDB T0335.try6-opt2.pdb
#ReadConformPDB T0335.try7-opt2.pdb
#ReadConformPDB T0335.try8-opt2.pdb
# ReadConformPDB T0335.try5-opt2.pdb
# ReadConformPDB T0335.try4-opt2.pdb	# similar to try7
# ReadConformPDB T0335.try2-opt2.pdb	# similar to try5
# ReadConformPDB T0335.try3-opt2.pdb	# similar to try6

InFilePrefix decoys/servers/
# ReadConformPDB SAM_T06_server_TS1.pdb
# ReadConformPDB ROBETTA_TS1.pdb

InFilePrefix 
# ReadConformPDB T0335.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
#ReadConformPDB T0335.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
#ReadConformPDB T0335.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
#ReadConformPDB T0335.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
#ReadConformPDB T0335.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 chimera-try8-opt2.pdb superpose \
	atom L76.CA atom H77.CA

#	atom Q30.CB atom Q31.CB atom K32.CB atom L33.CB \
#	atom R34.CB
	
# for attaching HIS tag:	


# 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