Dear Charles,
Thank you for the quick reply.
Indeed I dont use scale_toNH since my data are prescaled. So apparently
i do have to put them as raw (without prescaling) and let XPLOR scale
everything (both values AND weight of energy terms). Do i understand
correct?
The violations that I get are mainly ANGL violations not from RDCs.
thank you
Leonidas
On 06/03/2016 04:32 PM, Charles Schwieters 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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