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 T0293.a2m 1
 NameTarget T0293
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

// include best previously found decoys!
InFilePrefix decoys/
OutfilePrefix decoys/
// include read-pdb.under

# put believed-to-be-best decoy first
ReadConformPDB T0293.try5-opt2.pdb
# ReadConformPDB T0293.try4-opt2.pdb
# ReadConformPDB fromTry4.proto.pdb
# PrintConformSheets fromTry4.sheets
# ReadConformPDB T0293.try2-opt2.pdb

InfilePrefix decoys/servers/
# ReadConformPDB SAM_T06_server_TS1.pdb
# printConformSheets SAM_T06_server_TS1.sheets
# ReadConformPDB ROBETTA_TS5.pdb
# PrintConformSheets ROBETTA_TS5.sheets
# ReadConformPDB Pmodeller6_TS1.pdb
# PrintConformSheets Pmodeller6_TS1.sheets
# ReadConformPDB ROBETTA_TS4.pdb
# PrintConformSheets ROBETTA_TS4.sheets



InFilePrefix 
# ReadConformPDB T0293.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
ReadConformPDB T0293.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
# ReadConformPDB T0293.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
# ReadConformPDB T0293.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
# ReadConformPDB T0293.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 for-chimera1.pdb superpose \
	residue V226 residue P227 residue K228 residue V229 \
	residue R241 residue W242 \
	residue A243 residue L244 residue A245 residue W246

# 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