Hi Douglas-- > > I am trying to refine the NMR structure of three different stapled peptides > (you > may have seen my previous emails). For two out of three them, I have (with > Charles's help) managed to produce structures that match the expected helical > conformations, consistent with our CD data. > > The third is proving more problematic, in that there are no obvious error > messages being produced by Xplor, simply an "incorrect" structure. Our CD data > shows that this stapled peptide is adopting a helix, as it was designed to do, > but the structures coming out of Xplor have the stapled part disordered. > > Interestingly, if I refine using the same .tbl files but use an unstapled > model, > I get a helical conformation (and a lot fewer violations!). >
Doing a quick diff of the python scripts I see the use different parameter sets (the wt calculations use Xplor-NIH's default top/par values), and also the names of the restraint files are different. For that matter, even the number of residues differs. Please check that all is self-consistent. Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
