Hi,
My situation is the following : I have the structures of two
individual domains (determined by NMR with NOE data) that I have
merged into one structure via a linker (resulting in a 246 residues
protein).
The aim is now to correctly orient them. To do so, I have been using
RDC and SAXS data (from the full protein) and NOE data (from
individual domains) . I think that the RMSD and the ramachandran
statistics are not yet satisfactory. One problem is that, we had to
remove some NOE data (430 on 4000) for the residues which chemical
shifts changed too much between the individual and the linked form,
resulting in a loss of information of course.
Now, I was wondering how difficult it would be to use the information
coming from the variations of the chemical shifts between the
individual and linked forms and use it as ambiguous restraints ? The
idea is derived from the AIR definition of HADDOCK software.
So far, it is the only option I can think of to input new restraints
in my refinement calculation (without new acquisition). As it is the
first time I am doing a structure calculation, I lack experience and
background, and have limited knowledge on xplor-NIH, so any piece of
advice is welcome.
Thank you for your attention,
Best regards,
Olivier Serve, PhD
Postdoc
Okazaki Institute for Integrative Bioscience
National Institutes of Natural Sciences
5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
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