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

[William G. Scott]

HI Paul:

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.

Thanks.

Bill


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.
>
>   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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>
> -- 
> 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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> http://cci.lbl.gov/paul
>
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>
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