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

Kendall Nettles knettles at scripps.edu
Thu Dec 31 08:55:43 PST 2009

Hi Pavel,
 I am resetting the B factors in both cases. TLS definitely helps (does it every not help?).

If poor fit is the problem, why do I not see the variance with individual ADPs? I still don't think it makes physical sense to have one residue in a helix with an ADP of 100 and the next one with 200, which is what I'm seeing with the one per residue setting. With respect thermal motion, the adjacent residues are attached, so it makes sense to me to have their values restrained. I don't see how the rationale is different from individual ADPs.

On 12/31/09 11:40 AM, "Pavel Afonine" <PAfonine at lbl.gov> wrote:

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:
One adp per group gives very high variance between adjacent residues.  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?
Kendall Nettles


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