[phenixbb] Bulk Solvent

Jeff Headd jjheadd at lbl.gov
Tue Apr 17 08:18:39 PDT 2012

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?


On Tue, Apr 17, 2012 at 8:07 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  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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