# protocol module has many high-level helper functions. # import protocol protocol.initRandomSeed(1603) #set random seed - by time command = xplor.command # 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 = []
) elif os.path.exists(pdbFilename): psfGen.pdbToPSF(pdbFilename) # protocol.initCoords(pdbFilename) elif os.path.exists(psfFilename): # read in the PSF file and initial structure 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()
# protocol module has many high-level helper functions. # protocol.initRandomSeed() #set random seed - by time command = xplor.command # generate PSF data from sequence and initialize the correct parameters. # #seqToPSF('%s.seq'% pname) #Simply read the psf already generated. xplor.command("""struct @%s.psf end""" % pname) # 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. # potList = PotList() # parameters to ramp up during the simulated annealing protocol # rampedParams=[] highTempParams=[] ## compare atomic Cartesian rmsd with a reference structure ## backbone and heavy atom RMSDs will be printed in the output
) elif os.path.exists( pdbFilename ): psfGen.pdbToPSF(pdbFilename) # protocol.initCoords(pdbFilename) elif os.path.exists( psfFilename ): # read in the PSF file and initial structure 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()