Xplor Users,
I am using RDCs to refine an nmr structure and I want to make sure
I'm setting things up correctly. I have 1 bond CH and NH RDCs from the
same sample in the same alignment medium with the same measurement error.
1)RDCs for methyl groups were multiplied by a factor of -3 to compensate
for the effects of rotation, and the angle defined along the C-C bond.
(A bit of confusion here, some sources say multiply by -3, and some say
divide. Also, if I'm defining the methyl CH RDC using the C-C bond, do
I need to rescale the data relative to CC, and then again to NH?)
2)I scaled (by hand) the CH RDCs to NH by multiplying them by a factor
of about -1/2, using values for gyromagnetic ratios and bond lengths
from rdcPotTools.py, and the fact that the gyromagnetic ratio is
negative for Nitrogen and positive for Carbon.
3)I used gridsearch.inp to find two sets of Da and rhom values, one set
for the scaled CH data, and one for the NH data. (If I have to rescale
the methyl CH RDCs to CC, do I need a third set of Da and rhom values?)
4)Force constants for CH were multiplied by about 2 relative to NH (the
inverse of the scaling factor used in step 2)
Most of these steps have been culled the Xplor_nih mail archives but
theres always the chance that I've misunderstood a statement or two, so
if anyone has any suggestions or if one of these steps is simply wrong
I'd appreciate hearing about it.
Andrew Borgert
Graduate Student, Biophysical Sciences and Medical Physics
University of Minnesota
