[phenixbb] One adp per group gives very high variance between adjacent residues.

Pavel Afonine PAfonine at lbl.gov
Thu Dec 31 08:40:31 PST 2009

Hi Kendall,

when you do group isotropic ADP refinement no any ADP restrains are used.

Most likely this happens for residues not fitting electron density map 
well. I'm not sure what is the best approach here. Imagine one residue 
that fits density well and its group B-factor refines to a good value 
and the adjacent residue is out of density and, no surprises, its 
refined group B is very high. In this case if we apply restrains, we 
will spoil the group B-factor of the good residue by the high B-factor 
of the bad one, and we will force the high B of the bad residue to be 
unrealistically smaller than supported by the density.

Did you try resetting all B-factors to an average value before 
refinement (to make sure that what you are seeing is not a refinement 
artifact)? Also, you may want to try using larger groups: say, two 
residues per one refinable B (in this case you will need to give a long 
list of selections). You can try using TLS as well.

Individual ADP refinement may not be supported by the data amount 
(data-to-parameters ratio) at this resolution, as you see by 4% increase 
in Rfree (although, what happens with Rwork?).


On 12/31/09 8:01 AM, Kendall Nettles wrote:
> I playing around with ADP and TLS parameters for a 3.5 angstrom data 
> set. When I use one ADP per group, the values can vary by as much as 
> 100 between adjacent residues, which doesn't make physical sense to 
> me. If I refine individual ADPs this doesn't occur, but R free is 4% 
> higher. Is this a problem with my data, or something to do with the 
> implementation of this feature? Or something else?
> Best,
> Kendall Nettles
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