Hello,
Thank you for the explanation. I understood that there might be an
issue not with the docking itself but more probably between the
individual domains and their respective RDC's from the full protein
RDC experiment. As I wrote earlier, I am currently trying to refine
individual domains including RDC from the full protein experiment. I
have been using the standard refining script that you provide in the
eigeninput directory, and yet R-inf look quite high (~ 20 ) if I keep
Da and R fix, but it becomes much better if I allow those values to
change (Da changes from 5.5 to ~12 (or -12)).
I was wondering if, in that case, it does make sens or not to allow
Da and R to vary ? If not, there is a real issue (whatever it is) with
my RDC dataset or at least with the way I handle them. I have
recompared HSQC spectra from individual and linked domains (I have
been working only lately on the project), but the changes are not
important. So, I would have thought that RDC values would have maybe
only slightly modify orientations of secondary structures. All of this
is really intriguing.
Thanks again,
Best regards,
Olivier Serve, PhD
Postdoc
Okazaki Institute for Integrative Bioscience
National Institutes of Natural Sciences
5-1 Higashiyama, Myodaiji, Okazaki 444-8787
Japan
serve at ims.ac.jp
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