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

Pavel Afonine pafonine at lbl.gov
Mon Dec 20 21:35:43 PST 2010

  Hi Joe,

hmm... this is strange. I'm not in a convenient place to seriously look 
into this right now... but if you send me the data and model and tell 
which atoms are in problem, then I will have a look Thursday evening or 
Friday morning first thing (when I come back from vacation). I would 
like to know why kicked maps result in this effect and I want to fix 
this problem.


On 12/20/10 10:45 AM, Joseph Noel wrote:
> Pavel et al.,
> So it turns out I was generating "kicked" sigmaa weighted maps and not the traditional sigmaa weighted maps. When I return to the default mtz maps of phenix, then the positive density appearing on heavy atoms disappears. Has anyone seen similar results with kicked maps? One other thing, I have also unchecked the reject outliers option but in the results window of the GUI it still seems to be rejecting a few reflections. Is there a way to double check things to ensure no reflections are being rejected during refinements and map calculations?
> 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
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> 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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