[phenixbb] Bulk Solvent

Tue Apr 17 10:03:19 PDT 2012

difference density on the backbone can also arise (more often) due to suboptimal ADP refinement/restraints..or a bug in a particular build..

best wishes
roberto

PS I cc-ed this email to Garib in case he's got some info specific for 5.5.0102
On 17 Apr 2012, at 17:22, Timothy Springer wrote:

As I said, I cant say that, it is a guess based on two facts. 1) Looking at the output of refinement steps, and seeing that the largest decrease in R during refinement comes in the bulk solvent correction step. 2) It is also based on the common occurrence in the Refmac but not Phenix maps of negative difference density on backbone. This is a symptom of errors in bulk solvent correction.
Tim

On Apr 17, 2012, at 12:06 PM, Steiner, Roberto wrote:

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

Room 3.10A
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Guy's Campus
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Tel 0044-20-78488216
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Roberto Steiner, PhD
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.steiner at kcl.ac.uk<mailto:roberto.steiner at kcl.ac.uk>

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