[phenixbb] phenix.refine 1.3 vs. 1.4 map quality ?

Paul Adams PDAdams at lbl.gov
Thu Aug 6 09:57:51 PDT 2009

Hi Bill,

   I suspect that the maps in 1.3-rc6 do not use DFc for missing  
reflections, whereas in 1.4 they do by default. However, in version  
1.4 you can make non-filled maps in Coot using the other arrays in the  
map coefficient file. Could you try this to see if using the unfilled  
data makes your maps look more like the ones from 1.3b? This would be  
very interesting to us as we are still trying to assess the impact of  
filling in missing data. In addition, if you are using experimental  
phases in the refinement these will be used to make a phase combined  
map by default.


On Aug 6, 2009, at 7:43 AM, William G. Scott wrote:

> Hi folks:
> About a year ago I refined a 1.6 Å RNA structure with phenix.refine
> 1.3b-rc6 and then got distracted.  I picked it up today and
> essentially repeated the last round of refinement with 1.4-57 (and
> also 1.4-159).  The maps are subtly different, but consistently
> slightly worse with 1.4.
> Here are two examples:  http://sage.ucsc.edu/~wgscott/mystuff/old_vs_new.pdf
> In the second example, this would lead to deletion of one of the
> octahedrally coordinated waters on a known Mg++ ion.
> 2OEU is similar, except 2.0 Å resolution, and it has Mn2+ instead of  
> Mg
> ++.  A similar thing happens with the corresponding water in that
> structure.
> Has the weighting for the bulk solvent mask or something like that
> been increased?
> Thanks.
> Bill Scott
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Paul Adams
Acting Division Director, Physical Biosciences Division, Lawrence  
Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology

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