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Hello Lei--
> Is there a way (xplor script) to back calculate the rdcs from the pdb
> (including tensor values and principle axis) generated by xplor-nih? I
> generate a set of structures using N-HN rdcs and I would like to use the
> structure and tensor values to predict the C-HN rdcs.
sure. The attached (slightly modified) version of
eginput/protG/calcTensor.py will do this for you when run like this:
./calcTensor -printRDCs <rdc table file> <structure1> [structure2] ...
best regards--
Charles
#!/usr/bin/env pyXplor
# calculate Da and Rh from an ensemble of structures, given observed
# RDCs
#
usage = """
Calculate RDC alignment tensor using SVD given molecular structures
usage: calcTensor.py [options] <rdc.tbl> <pdb file1> [<pdb file2> ...]
where rdc.tbl is a file containing XPLOR-SANI-style assignment statements,
and pdb file1, ... are one or more structure file which have previously
been determined.
options:
--showRDCs - print out back-calculated RDC values
--fitSel <atom selection> - atom selection used to fit structures before
alignment tensor calculation.
"""
(optList, args) = xplor.parseArguments(["printRDCs:0",
"fitSel:1",
"help-script:0",])
#
# selection used to fit structures before tensor calculation
#
fitSel="name CA or name N or name C or name O"
printRDCs=False
for opt in optList:
if opt[0]=="showRDCs":
printRDCs=True
pass
if opt[0]=="fitSel":
fitSel=opt[1]
pass
if opt[0]=="help-script":
print usage
import sys
sys.exit(0)
pass
pass
if len(args)<2:
print usage
sys.exit(1)
pass
tables = args[0].split()
coordFiles = args[1:]
#
# specify a PSF file name, if you have one handy
#
psf=None
import protocol
if not psf:
from psfGen import pdbToPSF
pdbToPSF(coordFiles[0])
pass
from varTensorTools import create_VarTensor, calcTensor
from rdcPotTools import create_RDCPot, scale_toNH
from simulationTools import analyze
medium = create_VarTensor('medium')
coordArray=[]
from atomSelAction import Fit
fitCoords=None
for file in coordFiles:
protocol.initCoords(file)
if not fitCoords:
fitCoords = xplor.simulation.atomPosArr()
else:
if fitSel:
AtomSel("all").apply(Fit(fitCoords,fitSel))
pass
pass
coordArray.append( xplor.simulation.atomPosArr() )
pass
rdcs=[]
for table in tables:
rdcs.append( create_RDCPot(table,oTensor=medium,file=table) )
scale_toNH( rdcs[-1] )
rdcs[-1].setShowAllRestraints( True )
pass
tensor = calcTensor(medium,coords=coordArray)
#copy tensor atom positions
from atomSel import AtomSel
aniAtoms = AtomSel("resname ANI and resid %d" % medium.oAtom().residueNum())
aniPosAtoms = map(lambda a:(a.pos(),a), aniAtoms)
#print analyze(medium)
print "Da: %7.2f Rh: %7.3f" % (medium.Da() , medium.Rh())
print "Fit:"
for cnt in range(len(coordFiles)):
xplor.simulation.setAtomPosArr(coordArray[cnt])
#reset tensor atom positions
for (pos,atom) in aniPosAtoms:
atom.setPos(pos)
pass
print " %-20s " % coordFiles[cnt],
rdcs[0].calcEnergy()
print "%20s: %7.3f" % (tables[0], rdcs[0].rms()),
print
pass
#print tensor
# uncomment the next line to get a printout of back-calculated rdcs
if printRDCs:
print analyze(rdcs)
pass
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