[phenixbb] Standard settings for map generation in phenix.refine
tristan.croll at qut.edu.au
Tue Apr 21 02:53:34 PDT 2015
In the phenix.refine GUI, the default options for the maps auto-generated in Coot include the R-free set in the map coefficients. Is this the best choice? It's fairly natural for the user to immediately inspect/correct their structure using the helpfully-provided Coot window - which, as per a recent discussion thread on this list, can easily lead to over-fitting. I suspect I've been looking at such a case over the last week or so - a mid-3A structure refined in Phenix with an amazingly low Rfree (0.234) and Rfree-Rwork (~0.016), despite clear (albeit non-disastrous) errors in a number of loops, and moderate-poor statistics in structural quality metrics. Tellingly, the Rfree goes up quite substantially upon re-refinement after correcting these issues. If maps generated with the Rfree set included should only ever be used for final display, wouldn't it be better to have them excluded by default?
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