Garib's response below, since the server wouldn't let him post.
---------- Forwarded message ----------
From: Garib N Murshudov
To: "Steiner, Roberto"
Cc: PHENIX user mailing list
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. [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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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
[email protected]
_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb
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
[email protected]
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: [email protected]
Web http://www.mrc-lmb.cam.ac.uk
