Hi all, I'm trying to refine a structure where a portion of the protein does not have NOESY restraints associated with it. However, I would like to apply the database potentials so that the structures that I generate at least have reasonable ramachandran plots. However, if I use a standard krama of 1, it seems like my structures still have poor ramachandran statistics. If I increase krama to 20, I get better ramachandran stats, but I think that the number of violated NOE restraints have increased. Is there a way to restrain a portion of a protein with a stronger database potential while the rest of the protein is restrained with a weaker potential? I'm using a script modified from the refinement protocol in eginput/gb1_rdc.
Thanks, -Greg Zornetzer [email protected]
