[phenixbb] Bulk Solvent

[Timothy Springer]

no, it just takes me two years to write up sometimes--- So this is a historical question. But there is a ref in that powerpoint to following ref. If this was implemented in Phenix and not Refmac 2 years ago, I should cite it.

Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):850-5. Epub 2005 Jun 24.
A robust bulk-solvent correction and anisotropic scaling procedure.
Afonine PV, Grosse-Kunstleve RW, Adams PD.
Source
Lawrence Berkeley National Laboratory, One Cyclotron Road, Building 64R0121, Berkeley, CA 94720, USA. pafonine at lbl.gov
Tim


On Apr 17, 2012, at 11:18 AM, Jeff Headd wrote:

> 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 <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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