Dear Charles, dear all,
I'm refining some homology models using RDCs, dihedrals calculated by Talos+
and hydrogen bonds as restraints.
For the calculation of tensor parameters, i.e. Da and Rhombicity, I used
PALES and the Extended Histogram Method, implemented through nmrWish/nmrPipe
environment, for the sake of comparison. I'm actually working with a set of
RDCs from a single aligning medium involving the following nuclei couples:
CACO NCO and NH. I'm using XPLOR-NIH 2.25, through Python scripting.
The question is the following: what kind of definition of RDC should I have
to use for writing down the XPLOR-NIH input table from my peaklists?
I'm asking this because in the very beginning I fed XPLOR-NIH with a set
calculated as
RDC = |aligned splitting| - |isotropic splitting|
and activating the correctGyromagneticSign() function. In a second
experiment, I used the following definition:
RDC = sign(J)*( |aligned splitting| - |isotropic splitting| )
for introducing the correct signs due to the negative gyromagnetic ratio of
nitrogen directly in my input files. Needless to say,
the correctGyromagneticSign() function was avoided in this case.
As far as I understand the two solution should be equivalent. What I found
is that the sets of 4 Euler Angles for the two experiments are different
from each others. Doesn't the correctGyromagneticSign() function put a
negative sign to the Da prefactor anytime it finds a RDC where a nitrogen
atom is involved?
By the way, this is the part of the script relative to the RDCs (that one in
which correctGyromagneticSign() is turned on):
from varTensorTools import create_VarTensor
media={}
# medium Da rhombicity
for (medium,Da,Rh) in [ ('p', 9.393, 0.587)
]:
oTensor = create_VarTensor(medium)
oTensor.setDa(Da)
oTensor.setRh(Rh)
media[medium] = oTensor
pass
# dipolar coupling restraints for protein amide NH.
#
# collect all RDCs in the rdcs PotList
from rdcPotTools import create_RDCPot, scale_toNH, correctGyromagneticSigns
rdcs = PotList('rdc')
for (medium,expt,file, scale) in \
[('p','NH' ,'gyrNH_20110823.tbl' ,1),
('p','NCO' ,'gyrNCO_20110823.tbl' ,4.0),
('p','CACO' ,'gyrCAC_20110822.tbl' ,10.0)
]:
rdc = create_RDCPot("%s_%s"%(medium,expt),file,media[medium])
correctGyromagneticSigns()
rdc.setPotType('square')
scale_toNH(rdc)
rdc.setScale(scale)
rdc.setShowAllRestraints(1) #all restraints are printed during analysis
rdc.setThreshold(1.0) # in Hz
rdcs.append(rdc)
pass
potList.append(rdcs)
rampedParams.append( MultRamp(0.00005,2.8, "rdcs.setScale( VALUE )") )
Thanks in advance
Carlo
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20110825/dba46bd3/attachment.html
