[phenixbb] Bulk Solvent

Pavel Afonine pafonine at lbl.gov
Tue Apr 17 08:07:20 PDT 2012

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:


This is going to be published soon.


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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