segsResidues = getSegsResidues()
isDimer = False
if len(segsResidues) == 2:
idNames = list(segsResidues.values())
if idNames[0] == idNames[1]:
isDimer = True
print("found a h**o dimer")
pass
pass
#
# a PotList contains a list of potential terms. This is used to specify which
# terms are active during refinement.
#
from potList import PotList
potList = PotList()
# parameters to ramp up during the simulated annealing protocol
#
from simulationTools import MultRamp, StaticRamp, InitialParams
rampedParams = []
highTempParams = []
# compare atomic Cartesian rmsd with a reference structure
# backbone and heavy atom RMSDs will be printed in the output
# structure files
#
from posDiffPotTools import create_PosDiffPot
refRMSD = create_PosDiffPot("refRMSD", "name CA C N O", selection2="initial")
# generate PSF data from sequence and initialize the correct parameters.
#
from psfGen import seqToPSF
seqToPSF('protG.seq') ## modify ##
# generate random extended initial structure with correct covalent geometry
#
protocol.genExtendedStructure()
#
# a PotList contains a list of potential terms. This is used to specify which
# terms are active during refinement.
#
from potList import PotList
potList = PotList()
# parameters to ramp up during the simulated annealing protocol
#
from simulationTools import MultRamp, StaticRamp, InitialParams, IVMAction
rampedParams = []
highTempParams = []
# IVM setup
# the IVM is used for performing dynamics and minimization in torsion-angle
# space, and in Cartesian space.
#
from ivm import IVM
dyn = IVM()
minc = IVM() # minc used for final cartesian minimization
#Nilges topology/parameters
xplor.command('evaluate ($par_nonbonded = "OPLSX")')
protocol.parameters['protein']="waterRef/parallhdg5.3.pro.new"
protocol.parameters['water'] ="waterRef/parallhdg5.3.sol"
protocol.topology['protein'] ="waterRef/topallhdg5.3.pro.new"
protocol.topology['water'] ="waterRef/topallhdg5.3.sol"
waterResname="TIP3"
protocol.initParams(("protein","ion.par"))
#protocol.initStruct("zc2h2_waterref.psf")
protocol.loadPDB(inputStructures[0],deleteUnknownAtoms=True)
from potList import PotList
from simulationTools import MultRamp, StaticRamp, FinalParams
potList = PotList()
rampedParams=[]
# set up NOE potential
noe=PotList('noe')
potList.append(noe)
from noePotTools import create_NOEPot
for (name,scale,file) in [('all',1,"constraints/yourfolder/yourfoldernoe.tbl"),
#add entries for additional tables
]:
pot = create_NOEPot(name,file)
# pot.setPotType("soft") - if you think there may be bad NOEs
pot.setScale(scale)
noe.append(pot)
rampedParams.append( MultRamp(2,30, "noe.setScale( VALUE )") )
nefData = readNEF(nefFile)
from iupacNaming import toIUPAC, fromIUPAC
toIUPAC()
protocol.initCoords(cifFile)
protocol.addUnknownAtoms()
protocol.fixupCovalentGeom(maxIters=100,useVDW=1)
#
# a PotList contains a list of potential terms. This is used to specify which
# terms are active during refinement.
#
from potList import PotList
potList = PotList()
# parameters to ramp up during the simulated annealing protocol
#
from simulationTools import MultRamp, StaticRamp, InitialParams
rampedParams=[]
highTempParams=[]
# compare atomic Cartesian rmsd with a reference structure
# backbone and heavy atom RMSDs will be printed in the output
# structure files
#
from posDiffPotTools import create_PosDiffPot
refRMSD = create_PosDiffPot("refRMSD","name CA C N O",
pdbFile=cifFile)
command("structure @%s end" % psfFilename)
protocol.initParams("protein.par", weak_omega=1)
# command("coor @gb3_xray.pdb")
else:
print "ERROR: failed to find seq or psf file in %s" % os.getcwd()
sys.exit(1)
# end if
# generate a random extended structure with correct covalent geometry
protocol.genExtendedStructure(extFilename)
#
# a PotList conatins a list of potential terms. This is used to specify which
# terms are active during refinement.
#
potList = PotList()
# set up NOE potential
noe = create_NOEPot("noe", file=noeFilename)
noe.setPotType("soft")
noe.setRSwitch(0.5)
noe.setAsympSlope(1.)
noe.setSoftExp(1.)
noe.setThreshold(0.5)
print noe.info()
potList.append(noe)
# Set up dihedral angles
protocol.initDihedrals(
dihFilename,
scale=5, #initial force constant
command("structure @%s end" % psfFilename)
protocol.initParams("protein.par", weak_omega=1)
# command("coor @gb3_xray.pdb")
else:
print "ERROR: failed to find seq or psf file in %s" % os.getcwd()
sys.exit(1)
# end if
# generate a random extended structure with correct covalent geometry
protocol.genExtendedStructure(extFilename)
#
# a PotList conatins a list of potential terms. This is used to specify which
# terms are active during refinement.
#
potList = PotList()
# set up NOE potential
noe = create_NOEPot("noe",file=noeFilename)
noe.setPotType( "soft" )
noe.setRSwitch( 0.5 )
noe.setAsympSlope( 1. )
noe.setSoftExp(1.)
noe.setThreshold(0.5)
print noe.info()
potList.append(noe)
# Set up dihedral angles
protocol.initDihedrals(dihFilename,
scale=5, #initial force constant