Hello Krishna-- > > I have used XPLOR-NIH to refine the structure of a 29-mer peptide using the > wrefine.py script in the GB1 eginput directory, with RDC terms removed. It > generated structures with no violations. But when I tried to deposit the > structures, PDB detected planarity outliers. I am not sure what it means and > how > to fix this issue. Please kindly help to fix it. >
This likely means that one or more region which is expected to be planar is not- the validation report should report which atoms are problematic. First, I would like to see the coordinates, to see if there is a problem with the parameters used in the water refinement script. If you could send me these, I can probably quickly fix things up. Another option you have is to instead use the implicit solvent script refine_eefx.py in the same directory. Of course, I suggest the latest release (version 2.45) for the best results. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
