After experimenting a bit:
Dihedral Angle restrains + NC rdcs (let Da and R float)--> good result with no
violations and r-factor 0.14 (Da found 49 and R 0.249)
from rdcPotTools import create_RDCPot,
rdcs = PotList('rdc')
for (medium,expt,file, scale) in \
[('l','NCO','RDC_nc_tpr_cns_noloops.tab' ,1)
]:
rdc = create_RDCPot("%s_%s"%(medium,expt),file,media[medium])
Dihedral angle restrains + NH rdcs (let Da and R float again) --> good result
no violations with r-factor for NHs fitting 0.41 (Da found 24 and R 0.4)
from rdcPotTools import create_RDCPot,
rdcs = PotList('rdc')
for (medium,expt,file, scale) in \
[('l','NH' ,'RDC_hn_tpr_cns_noloops.tab' ,1),
]:
rdc = create_RDCPot("%s_%s"%(medium,expt),file,media[medium])
But when I use both RDC from NHs and NCs i get many ANGL violations.
The fact that i get two different Values for Da and R depending on the data
set, should ring any bell on how should i treat them when i combine them?
thank you
Leonidas
On Jun 3, 2016, at 5:06 PM, Gabriel Cornilescu wrote:
Additionally, the relative sign of the RDCs (due to various sign conventions
for 15N) may get inadvertently flipped, so it’s a good idea to test refining
with each RDC set separately. Or, you can SVD fit the carbon RDCs them to a
model structure that fits well the NHs and pay attention to the sign of the
best fitting alignment tensor axes sign etc. Sometimes empirically flipping the
sign of the NH RDCs when SVD fitting in conjunction with say CaC would result
in a much better fit, proving that their (intial) relative sign was wrong.
Cheers,
Gabriel
On Jun 3, 2016, at 9:32 AM, Charles Schwieters
<[email protected]<mailto:[email protected]>> wrote:
Hello Leonidas--
I am trying to refine a crystal structure with RDCs, including NH, NC,
and CaC (and dihedral angles). While NHs and dihedral angles give nice
result, when I include any of the carbon RDCs the algorithm does not
converge due to many violations. I wonder if there is any method to
weight different thos NC and CaC RDCs to influence less than the NH,
if that makes sense.
1) Please read the paragraph at the top of
https://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/rdcPotTools.html
about the RDC sign convention.
2) If you prescale the RDCs (don't use scale_toNH), then you usually
will need to weight the energy terms differently, but if you do not
prescale the RDCs (and thus use scale_toNH in the script), the
energies of the RDCs involving different nuclei should scale
appropriately (such that signal to noise is approximately the same)
without different weight factors.
3) The number of violations is not such a useful concept for RDCs, as
the threshold for violation would generally be different for those
of large and small magnitude. Thus, we usually use the R-factor (or
possibly chi^2) to assess the goodness of RDC fit.
I hope this helps--
Charles
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