I don't know what a kicked map is, but filling is done with a best estimate for missing reflections. (Treating them as zero is a bad thing.) On Aug 6, 2009, at 10:54 AM, Francis E Reyes wrote:
Filled and non filled maps? Kicked maps?
Is there documentation on what these are ?
Thanks
FR
On Aug 6, 2009, at 10:57 AM, Paul Adams wrote:
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.
Cheers, Paul
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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