[phenixbb] (no subject)

Pavel Afonine 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.


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