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Hi Kendall,<br>
<br>
when you do group isotropic ADP refinement no any ADP restrains are
used. <br>
<br>
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.<br>
<br>
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.<br>
<br>
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?).<br>
<br>
Pavel.<br>
<br>
<br>
<br>
On 12/31/09 8:01 AM, Kendall Nettles wrote:
<blockquote cite="mid:C76234FA.7AE4%25knettles@scripps.edu" type="cite">
<title>One adp per group gives very high variance between adjacent
residues. </title>
<font face="Calibri, Verdana, Helvetica, Arial"><span
style="font-size: 11pt;">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? <br>
Best, <br>
Kendall Nettles<br>
</span></font>
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