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%20b... 2005 Jul;61(Pt 7):850-5. Epub 2005 Jun 24.
A robust bulk-solvent correction and anisotropic scaling procedure.
Afonine PVhttp://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed?term=%22Afonine..., Grosse-Kunstleve RWhttp://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed?term=%22Grosse-..., Adams PDhttp://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/pubmed?term=%22Adams%2....
Source
Lawrence Berkeley National Laboratory, One Cyclotron Road, Building 64R0121, Berkeley, CA 94720, USA. [email protected]mailto:[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 mailto:[email protected]> 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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