Hello Qi-- > > I am recently dealing with a problem of ensemble average of multidomain > protein > against RDC data and PRE data as well. > > We wanted to find an ensemble that best fit to the RDC and PRE data, as no > single > conformation was found satisfying the experimental data. I gave tries with the > script included in Xplor eginput/sardc folder although the results were not > good. > For ensemble size from 2 to 4, I did not see big differences between the > conformations. We would expect generally two distinct conformations, one is > close, the other is more open. Although the results gave only closed > conformation, which resembles the input structure. I am not sure if the script > fits my case. > > In the meantime, I realized that my case is similar to 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¡V16147 (2013). >
The scripts used in that work are included in the eginput/capsid subdirectory of the recent releases of Xplor-NIH. This script requires you to identify a linker and rigid subdomains in the calculation. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
