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%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