[phenixbb] Geometry Restraints - Anisotropic truncation
Frank von Delft
frank.vondelft at sgc.ox.ac.uk
Tue May 1 23:53:17 PDT 2012
>>> 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
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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