Hello,
I am trying to figure out how to obtain statistics regarding them
(rdcPotTools RDC_analyze?). I have successfully run a structure
calculation using RDCs; in my stats table I get violations and an
RMSD(dev). Are these the only values available? Is there a way to see the
average R-factor in this table as well (or is it likely there and I am
missing it)?
Any help would be greatly appreciated! I haven't been able to find
anything in the mailing list archives or otherwise online that I can
successfully implement.
Thank you,
Colleen
The section of my current refine.py script implementing the RDCs as well
as the section at the end that creates my output table is below:
# dipolar coupling restraints for protein amide NH.
#
# collect all RDCs in the rdcs PotList
#
# RDC scaling. Three possible contributions.
# 1) gamma_A * gamma_B / r_AB^3 prefactor. So that the same Da can be used
# for different expts. in the same medium. Sometimes the data is #
prescaled so that this is not needed. scale_toNH() is used for this.
# Note that if the expt. data has been prescaled, the values for rdc
rmsd
# reported in the output will relative to the scaled values- not the
expt.
# values.
# 2) expt. error scaling. Used here. A scale factor equal to 1/err^2 #
(relative to that for NH) is used.
# 3) sometimes the reciprocal of the Da^2 is used if there is a large #
spread in Da values. Not used here.
#
from rdcPotTools import create_RDCPot, scale_toNH
rdcs = PotList('rdc')
for (medium,expt,file, scale) in \
[('b','NH' ,'081218_CytRDBD_orgbicll_nh.tbl' ,1),
]:
rdc = create_RDCPot("%s_%s"%(medium,expt),file,media[medium])
#1) scale prefactor relative to NH
# see python/rdcPotTools.py for exact calculation
# scale_toNH(rdc) - not needed for these datasets -
# but non-NH reported rmsd values will be
wrong.
#3) Da rescaling factor (separate multiplicative factor)
# scale *= ( 1. / rdc.oTensor.Da(0) )**2
rdc.setScale(scale)
rdc.setShowAllRestraints(1) #all restraints are printed during
analysis
rdc.setThreshold(1.5) # in Hz
rdcs.append(rdc)
pass
potList.append(rdcs)
rampedParams.append( MultRamp(0.05,5.0, "rdcs.setScale( VALUE )") )
# calc. initial tensor orientation
#
from varTensorTools import calcTensorOrientation
for medium in media.values():
calcTensorOrientation(medium)
pass
-----------------
from simulationTools import StructureLoop
StructureLoop(numStructures=numberOfStructures,
pdbTemplate=outFilename,
structLoopAction=calcOneStructure,
genViolationStats=1,
averageTopFraction=0.1, #report stats on best 50% of structs
averageSortPots=[potList['BOND'],potList['ANGL'],potList['IMPR'],
noe,rdcs,potList['CDIH']],
averageFilename="SCRIPT_ave.pdb", #generate regularized
ave structure
averagePotList=potList).run()
