Hello Qingguo--
> I am recently using Xplor-NIH to refine one of our NMR structure > based on some global restraints such as RDC and SAXS. Our system is > a protein containing two rigid domains connected by a long flexible > linker. We detected no NOE between two domains, and we had many > evidence that that these two domains don’t have a fixed relative > orientation. We had our structure submitted for publication recently > and received the suggestion from the reviewer that we should refine > our overall structure using RDC and SAXS to generate a ensemble > representation. We then collected RDC and SAXS, applied them for > ensemble determination using Xplor-NIH. However, due to the RDC > restraints, the relative orientation of two domains in the all > ensemble structures are basically same, which doesn't seem to > reflect a real situation. I am wondering if there are some options > in Xplor, which allow us to generate multiple structures, and only > their average will meet the RDCs. Your early reply will be highly > appreciated. Have you tried using the ensembleSimulation functionality? Do you have RDCs in a steric aligning medium (like bicelles)? If you you might see the example in the eginput/sardc directory of the Xplor-NIH distribution. More similar to your problem is the work published in L. Deshmukh, C.D. Schwieters, A. Grishaev, R. Ghirlando, J.L. Baber, and G.M. Clore, ``Structure and Dynamics of Full-Length HIV-1 Capsid Protein in Solution,'' J. Am. Chem. Soc. 135, 16133–16147 (2013). I don't yet have the script for this in the distribution, but if you think they'd be useful, I'll send you a copy. This approach does not work so well for RDCs measured in charged media, as the alignment tensors are simply fit parameters in those cases. If your domains align separately, then there must be different alignment tensors for each domain, and there would be no reason for the two domains to have a constant relative orientation. So I don't understand that result. One final point: if the SAXS data fit a single conformation, they will be of little help in determining an ensemble. I hope this helps-- Charles _______________________________________________ Xplor-nih mailing list Xplor-nih@cake.cit.nih.gov http://cake.cit.nih.gov/mailman/listinfo/xplor-nih
