nefFile = opt[1]
pass
if opt[0] == "cif": #specify -quick to just test that the script runs
cifFile = opt[1]
pass
pass
from os.path import splitext
id = splitext(nefFile)[0]
# protocol module has many high-level helper functions.
#
import protocol
protocol.initRandomSeed(3421) #explicitly set random seed
protocol.initParams("protein")
from glob import glob
for topFile in glob('*.top'):
protocol.initTopology(topFile)
pass
for parFile in glob('*.par'):
protocol.initParams(parFile)
pass
import psfGen
psfGen.addResidueName("ACD", "metal")
# generate PSF data from sequence and initialize the correct parameters.
#
#from psfGen import seqToPSF
#seqToPSF('protG.seq')
#protocol.initStruct("g_new.psf") # - or from file
simWorld.setRandomSeed( 785 )
import protocol
backbone="name C or name CA or name N or name O or name HN"
#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"),
pass
if opt[0]=="cif": #specify -quick to just test that the script runs
cifFile=opt[1]
pass
pass
from os.path import splitext
id=splitext(nefFile)[0]
# protocol module has many high-level helper functions.
#
import protocol
protocol.initRandomSeed(3421) #explicitly set random seed
protocol.initParams("protein")
# generate PSF data from sequence and initialize the correct parameters.
#
#from psfGen import seqToPSF
#seqToPSF('protG.seq')
#protocol.initStruct("g_new.psf") # - or from file
# or read an existing model
#
from nefTools import readNEF
nefData = readNEF(nefFile)
from iupacNaming import toIUPAC, fromIUPAC
toIUPAC()
seq = open(seqFilename).read()
seqToPSF(
seq, # Customize here for specific settings or get them from a dictionary with the project or so.
startResid=1,
deprotonateHIS=1,
segName='',
disulfide_bonds=[],
disulfide_bridges=[],
)
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()
if os.path.exists( seqFilename ):
seq = open(seqFilename).read()
seqToPSF(seq, # Customize here for specific settings or get them from a dictionary with the project or so.
startResid=1,
deprotonateHIS=1,
segName='',
disulfide_bonds=[],
disulfide_bridges=[],
)
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()
nefFile = opt[1]
pass
if opt[0] == "cif": #specify -quick to just test that the script runs
cifFile = opt[1]
pass
pass
from os.path import splitext
id = splitext(nefFile)[0]
# protocol module has many high-level helper functions.
#
import protocol
protocol.initRandomSeed(3421) #explicitly set random seed
protocol.initParams("protein")
# generate PSF data from sequence and initialize the correct parameters.
#
#from psfGen import seqToPSF
#seqToPSF('protG.seq')
#protocol.initStruct("g_new.psf") # - or from file
# or read an existing model
#
from nefTools import readNEF
nefData = readNEF(nefFile)
protocol.initStruct("ACD.psf", erase=False)
protocol.initParams("ACD.par")