[phenixbb] phenix.refine 1.3 vs. 1.4 map quality ?
William G. Scott
wgscott at chemistry.ucsc.edu
Thu Aug 6 11:11:21 PDT 2009
I haven't had a chance yet but will do so today.
I think I answered the rest in the other email just cc-ed to you.
On Aug 6, 2009, at 9:57 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.
> 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
>> ++. A similar thing happens with the corresponding water in that
>> Has the weighting for the bulk solvent mask or something like that
>> been increased?
>> Bill Scott
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> 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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