[phenixbb] Geometry Restraints - Anisotropic truncation

Frank von Delft frank.vondelft at sgc.ox.ac.uk
Tue May 1 23:53:17 PDT 2012

Hi Pavel

>>> In general, given highly anisotropic data set:
>>> 1) maps calculated using all (unmodified) data by phenix.refine,
>>> phenix.maps and similar tools are better than maps calculated using
>>> anisotropy truncated data. So, yes, for the purpose of map calculation
>>> there is no need to do anything: Phenix map calculation tools deal with
>>> anisotropy very well.
>> If there are a lot of reflections without signal, that makes them 
>> essentially missing, so by including them, you're effectively filling 
>> in for those reflections with only DFc.  If anisotropy is very strong 
>> (i.e. many missing reflections), does that not introduce very 
>> significant model bias?  The maps would look cleaner, though.
> That's a different story. If you do anisotropy truncation then in case 
> of severe anisotropy there will be lots of removed weak Fobs, which 
> will be subsequently filled in with DFc, and such maps will have a 
> better chance to be more model biased. However, phenix.refine always 
> creates two 2mFo-DFc maps: with and without filling missing Fobs, so 
> you can quickly compare them and get an idea.
No, the comparison I mean is

     no anisotropy cut-off /--vs-- /anisotropy cut-off WITHOUT filling 
in missing reflections.

I'm wondering about what happens when you do NOT do anisotropy 
truncation:  that generates large volumes of reciprocal space where Fobs 
is approximately zero, and therefore the map coefficients (2mFo-DFc) 
become DFc -- i.e. the equivalent to filling in missing Fobs for very 
incomplete data.

The maps to compare would be:

(Of course, it presumably matters how effectively D down-weights those 
reflections;  but how is calculation of D affected by a resolution bin 
being dominated by near-zero Fobs?)

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