[phenixbb] (no subject)

Sneha Rangarajan rsneha at umd.edu
Fri Oct 3 11:58:17 PDT 2014

Thanks for your suggestions.

I did another round of refinement with default settings (XYZ,realsp, IndB and occ) with and without weight optimization.

Without weight opt, the Rfactors are 23/36 with RMSbonds-0.0108 and RMSangles-1.750

With weight optimization (Xray stereo and Xray ADP) the Rfactors are 32/39 with RMSbonds-0.0052 and RMSangles-1.390.

I am now going to try running simulated annealing along with weight optimization and see if that makes a difference.


From: Pavel Afonine [mailto:pafonine at lbl.gov]
Sent: Friday, October 03, 2014 2:30 AM
To: Nathaniel Echols; Sneha Rangarajan
Cc: phenixbb at phenix-online.org
Subject: Re: [phenixbb] (no subject)


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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