[phenixbb] ADP restraints - distance power, average power, etc

Ed Pozharski epozh001 at umaryland.edu
Mon Dec 20 11:01:26 PST 2010

Refine with refmac and see if the positive density shows up there too.
If it does, then either there is something peculiar about your structure
or both programs suffer from the same bug that somehow only shows up
with your particular dataset.  If not, then it is indeed phenix bug
(still rather specific to your dataset).

Are positive density peaks centered around the corresponding atoms?

Not sure what you mean by saying that peaks "extend to 4 sigma".

To verify your suspicion about ADP weights, consider manually resetting
B-factor of, say, one of the offending sulfurs and calculating the
corresponding map.

On Mon, 2010-12-20 at 09:06 -0800, Joseph Noel wrote:
> Hi Pavel,
> I've refined individual ADPs (anisotropic for the protein and isotropic for solvent). Still quite a bit of positive density on methionine sulfurs and most carbonyls. They start around 7.5 sigma and extend to 4 sigma. There are no other Fo-Fc peaks appearing for solvent yet to be modeled, etc. so maybe I should play with ADP weights. All positive density is appearing on atoms with occupancies of 1 so not much more I can do to lower the positive density. 
> Joe
> ___________________________________________________________
> Joseph P. Noel, Ph.D.
> Investigator, Howard Hughes Medical Institute
> Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics
> The Salk Institute for Biological Studies
> 10010 North Torrey Pines Road
> La Jolla, CA  92037 USA
> Phone: (858) 453-4100 extension 1442
> Cell: (858) 349-4700
> Fax: (858) 597-0855
> E-mail: noel at salk.edu
> Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37
> Web Site (HHMI): http://hhmi.org/research/investigators/noel.html
> ___________________________________________________________
> On Dec 19, 2010, at 5:12 PM, Pavel Afonine wrote:
> > Hi Joe,
> > 
> > at 1.45A resolution it is most likely the best to refine individual anisotropic ADPs using phenix.refine (anisotropic for macro-molecule and isotropic for the solvent). In that case the "local sphere restraints" are not used ("local sphere restraints" are used in individual isotropic ADP refinement only). All the relevant details are here:
> > 
> > see "On atomic displacement parameters (ADP) and their parametrization in PHENIX" article:
> > 
> > http://www.phenix-online.org/newsletter/
> > 
> > I'm almost sure that refining isotropic ADPs instead of anisotropic causes these residual densities around atoms. It's known effect and I recall seeing it in at least two papers.
> > 
> > Another things to check:
> > 
> > - is it Met, or Se-Met?
> > - radiation damage? Try refining occupancies of S. Although you said it's not only S, so may be not.
> > 
> > Good luck!
> > Pavel.
> > 
> >> I am refining a very well ordered structure at 1.45 A and find that after doing just about everything including optimization of weights, etc that there are still areas of positive density residing over S atoms of Met, backbone atoms, etc. I have added hydrogens and used them during refinement as well. The maps are of a high quality and Free R factors are quite good, ~ 17%. Is there anything that can be played with more such as values used in the ADP restraints window to try and achieve a difference map with far fewer areas of significant positive density (all greater then or equal to 4 sigma)?
> >> 
> >> I am not sure exactly what effect the values of distance power, average power, etc will have on refinement. The other option I was thinking of was the scattering table options. I have other structures of this protein that extend to about 1.2.
> > 
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