Re: [phenixbb] Bulk Solvent

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. [email protected] 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 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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