Hi Tim,
If you are using Phenix 1.5.2, that would not have had the new bulk-solvent
model that Pavel is talking about. Are you using that old of a version for
your tests?
Jeff
On Tue, Apr 17, 2012 at 8:07 AM, Pavel Afonine
Hi Tim,
this is because recently (a few weeks ago) we introduced a novel bulk-solvent model and a new overall anisotropic scaling procedure.
Some detailed overview is here:
http://www.phenix-online.org/presentations/PhenixSantaFe2012_PA.pdf
This is going to be published soon.
Pavel
On 4/17/12 7:59 AM, Timothy Springer wrote:
In one of the structures I have refined, I found phenix 1.5_2 gave 1 to 1.5% lower Rfree and Rwork than REFMAC 5.5.0102. Can I propose in a publication that "We attribute these differences to methods for handling bulk solvent in PHENIX that are less adversely affected by deficiencies in the crystallographic data."? This is a guess, because there is a large contribution to refinement from bulk solvent, rather than factual information. I did cross-refinement, and found it going from structures refined in REfmac to Phenix, and vice versa. The Phenix maps looked better, too. Is this a reasonable suggestion, and would there be a relevant reference? Tim
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