[phenixbb] Bulk Solvent

Tue Apr 17 10:15:54 PDT 2012

Garib's response below, since the server wouldn't let him post.

---------- Forwarded message ----------
From: Garib N Murshudov <garib at MRC-LMB.CAM.AC.UK>
To: "Steiner, Roberto" <roberto.steiner at kcl.ac.uk>
Cc: PHENIX user mailing list <phenixbb at phenix-online.org>
Date: Tue, 17 Apr 2012 18:11:24 +0100
Subject: Re: [phenixbb] Bulk Solvent
Dear all

I cannot say much without data. Only thing I can say that there were
some problems in some of the versions in 5.5, and there are some
improvements in recent versions.
5.7 series may perform better.
Before claiming that improvement is due to particular feature I would
do a little bit more analysis.

regards
Garib

On 17 Apr 2012, at 18:03, Steiner, Roberto wrote:

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. 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
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>

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<ATT00001..c>

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

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<ATT00001..c>

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

Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: garib at mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk