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Hi Jianghai,<br>
<br>
I see now. The problem is that if you do individual B-factors
refinement (no TLS) then the result will be affected by restraints.
Ideally you would need to do this without restraints, but this is not
practical. <br>
<br>
To obtain the estimate you want I would simply do group B-factors
refinement with one B per residue. In this case the restrains are not
used. It would be good to compare the results with TLS and individual
only refinement. Do it in two steps: re-set all B to Wilson B (or to
current average), then do group B refinement:<br>
<br>
1) phenix.pdbtools model.pdb set_b_iso=25<br>
2) phenix.refine model_b25.pdb data.mtz strategy=group_adp<br>
Note, the default is one B per residue. You can specify your own
selections.<br>
<br>
Pavel.<br>
<br>
<br>
On 5/11/2008 7:00 AM, Jianghai Zhu wrote:
<blockquote
cite="mid:F1724790-648D-4020-ADE5-783C43A7126D@idi.harvard.edu"
type="cite">
<pre wrap="">Pavel,
Thanks. I actually just want to do a very simple thing. In the days
before TLS refinement, we use B-factor distributions to find the
ordered and less ordered regions in the structure, i.e. low B-
factors, ordered region and high B-factors, less ordered region. I
just wondered if I can still do that with the isotropic equivalent B-
factors after a TLS refinement. Or should I just get a real isotropic
B-factors distribution by re-refining the model without TLS?
-- Jianghai
On May 11, 2008, at 2:03 AM, Pavel Afonine wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Jianghai,
</pre>
<blockquote type="cite">
<pre wrap="">If I compare the isotropic equivalent B-factor
after TLS refinement to the isotropic B-factor without TLS
refinement,
will they have the same trend?
</pre>
</blockquote>
<pre wrap="">yes, only if:
1) the choice of TLS groups is correct;
2) the restraints on isotropic individual B-factors are not too tight.
</pre>
<blockquote type="cite">
<pre wrap="">I want to use the B-factor
distribution to describe the ordered and disordered region in the
structure, will the TLS refinement skew that?
</pre>
</blockquote>
<pre wrap="">I'm not sure what exactly you want to do here. But anyway, by using
TLS
model you better describe atomic ADP: TLS models global domain motion
and individual B-factors model local atomic vibrations; that is each
kind of motion receives dedicated parameterization (which is good).
However, if you model everything with individual B-factors (no TLS)
the
similarity restraints are always used and they tend to remove TLS
contribution making final B-factors less adequate.
Pavel.
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