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Hi Kendall,<br>
<br>
<blockquote cite="mid:C76241BF.7AEE%25knettles@scripps.edu" type="cite"><font
face="Calibri, Verdana, Helvetica, Arial"><span
style="font-size: 11pt;"> I am resetting the B factors in both cases.
TLS definitely helps (does it every not help?). <br>
</span></font></blockquote>
<br>
The goal of using TLS model is not to reduce R-factor, but is to use
more physically correct model (this is primary), and eventually reduced
R-factor (this is secondary) is the reward for doing so; while
increased R-factor will indicate the incorrect ADP model.<br>
<br>
<blockquote cite="mid:C76241BF.7AEE%25knettles@scripps.edu" type="cite"><font
face="Calibri, Verdana, Helvetica, Arial"><span
style="font-size: 11pt;">If poor fit is the problem, why do I not see
the variance with individual ADPs? </span></font></blockquote>
<br>
Because the ADP restraints are used in case of individual ADP
refinement, and no restrains are used in case of group B refinement.
Did you try refining individual ADPs with two scenarios:<br>
- using "wxu_scale=true" to optimize weights;<br>
- manually setting very string ADP restraints ?<br>
I would definitely try both options.<br>
<br>
<blockquote cite="mid:C76241BF.7AEE%25knettles@scripps.edu" type="cite"><font
face="Calibri, Verdana, Helvetica, Arial"><span
style="font-size: 11pt;">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, </span></font></blockquote>
<br>
I did not say it is correct or makes physical sense. I just tried to
explain why it happens (the most likely reason).<br>
<br>
<blockquote cite="mid:C76241BF.7AEE%25knettles@scripps.edu" type="cite"><font
face="Calibri, Verdana, Helvetica, Arial"><span
style="font-size: 11pt;">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. </span></font></blockquote>
<br>
Copy-paste from my previous email:<br>
"""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>
which is saying differently : If both residues fit density well, then
applying restraints will not do any harm, and this is not the case
otherwise.<br>
<br>
If in your particular case both residues fit density very good and the
difference between their refined group B-factors is very large, then
the problem is somewhere else, and this needs more investigation (which
may take a day or more). Also, I will need to be able to reproduce it
myself (I need the data and model for this). I will see what it takes
to add restrains for group B refinement, at least for experimenting.<br>
<br>
Pavel.<br>
<br>
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