[phenixbb] Let's talk about maps...Re: phenix.refine 1.3 vs. 1.4 map quality ?

[William G. Scott]

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
>>>
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>> -- 
>> 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
>>
>> Building 64, Room 248
>> Tel: 1-510-486-4225, Fax: 1-510-486-5909
>> http://cci.lbl.gov/paul
>>
>> Lawrence Berkeley Laboratory
>> 1 Cyclotron Road
>> BLDG 64R0121
>> Berkeley, CA 94720, USA.
>>
>> Executive Assistant: Patty Jimenez [ PAJimenez at lbl.gov ]
>> [ 1-510-486-7963 ]
>> --
>>
>>
>>
>>
>>
>>
>>
>>
>>
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>
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
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