[phenixbb] (no subject)
pafonine at lbl.gov
Thu Oct 2 23:29:48 PDT 2014
> 1) When is a good time to start building the peptide into the
> density (should I wait until Rfactors improve significantly)?
> I would advise waiting until the rest of the model is as good as
> possible. That way you can use the difference map as a paper figure
> without needing to do any extra refinement to remove model bias later.
It's good to keep in mind that in this case map will be biased by the
non-atomic model (bulk-solvent), as well as by the atomic model as shown
here: Acta Cryst. (2002). A58, 270-282.
Also note, more (correct) model you build - better map you get - so even
more model you can build.
> 3) What is a general good strategy for lowering Rfactors? (Esp if
> the gap between Rwork and Rfree is high..like 28/40 or so)?
28/40 sounds worrying. In majority of scenarios I've seen so far such a
big difference between Rfree and Rwork indicates a problem that is
typically out of scope of refinement.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb