I dont think you need to worry much about the strong stacking
reflections; TRUNCATE really only modifies the weakest data - and
anything > 3Sigma is barely altered . There is a slightly wrong estimate
of <sigma> for that resolution shell, but in practice it seems to have
no observable effect..
Anisotropy is another question and drastically increases the number of
weak reflections in the higher resolution shells which must be bad.. Ian
- have you analysed any such data sets?
And if there are differences between maps from different programs, these
often seem to be due to different scaling algorithms and weighting for
the large Fo/Fc differences.. When we can study the loggraphs of <Fo>
and <Fc> v resolution it sometimes highlights such problems
Eleanor
William G. Scott wrote:
> On Sep 9, 2008, at 8:12 AM, Phoebe Rice wrote:
>
>> Thanks for all the interesting answers so far!
>>
>> The anisotropy issue is one that got me worrying about
>> truncate for data from DNA-containing crystals in
>> particular - and the fact that since its a default in ccp4i,
>> new people have stopped worrying about whether or not they
>> should use it.
>>
>> The DNAs usually stack end-to-end, and thus are very often
>> aligned with a particular axis. Since all those nice flat
>> bases are ~3.4A apart, there are often whomping spots in
>> only one direction at ~3.4A (even if the DNA isn't even half
>> the total scattering mass). So even if the overall
>> diffraction limits are roughly isotropic, in certain
>> resolution shells isotropy is still a bad assumption.
>>
>> Phoebe
>>
>
> We have a similar phenomenon with RNA, even if it is more globular.
>
> If I refine with phenix.refine on I's rather than F's, and avoid
> truncate, I have noticed the maps look slightly different. In one
> case the Mn cluster at 2.0 Å resolution is better defined in the
> sigmaA-weighted 2Fo-Fc map made from truncate/refmac than it is in the
> sigmaA-weighted 2Fo-Fc map made from phenix.refine.
>
> I wonder if truncate is actually helping more than hurting in this case?
>
>
>
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