[phenixbb] Bulk Solvent

[Steiner, Roberto]

Hi Tim,

How can you say the difference is really down to bulk solvent correction? there's several other parameters that affect differences in R factors....

Just curious
R
On 17 Apr 2012, at 16:27, Timothy Springer wrote:

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.<http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed?term=robust%20bulk%20solvent%20correction#> 2005 Jul;61(Pt 7):850-5. Epub 2005 Jun 24.
A robust bulk-solvent correction and anisotropic scaling procedure.
Afonine PV<http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed?term=%22Afonine%20PV%22%5BAuthor%5D>, Grosse-Kunstleve RW<http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed?term=%22Grosse-Kunstleve%20RW%22%5BAuthor%5D>, Adams PD<http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed?term=%22Adams%20PD%22%5BAuthor%5D>.
Source
Lawrence Berkeley National Laboratory, One Cyclotron Road, Building 64R0121, Berkeley, CA 94720, USA. pafonine at lbl.gov<mailto: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<mailto: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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Roberto Steiner, PhD
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London

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