[phenixbb] phenix.refine 1.3 vs. 1.4 map quality ?
William G. Scott
wgscott at chemistry.ucsc.edu
Thu Aug 6 07:43:15 PDT 2009
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
Has the weighting for the bulk solvent mask or something like that
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