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

[William G. Scott]

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