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Just to add to Nat's reply (which is 100% correct): even when you
refine group B-factors and nothing else, the mutual distribution of
B-factors withing the group remains the same but it is a constant
correction that is the refinable parameter. <br>
<br>
For example, if for residue A the B-factors before group-B refinement
were: 5,6,7,8.<br>
Then after group-B refinement they can be 7,8,9,10 or 2,3,4,5; where in
the first case the individual overall B-factor correction was 2 and in
the second case it was 3.<br>
<br>
Cheers,<br>
Pavel.<br>
<br>
<br>
On 3/5/09 10:00 AM, Nathaniel Echols wrote:
<blockquote cite="mid:4B1BD2CB-D0B7-4474-AB21-CB3C7ACFAD25@lbl.gov"
type="cite">
<pre wrap="">(I think the server must have a lag time between adding a new email
address and accepting posts from it. . .)
</pre>
<blockquote type="cite">
<pre wrap="">From: Roeland Boer <a class="moz-txt-link-rfc2396E" href="mailto:rbocri@ibmb.csic.es"><rbocri@ibmb.csic.es></a>
Date: March 5, 2009 5:29:19 AM PST
To: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
Subject: TLS without isotropic adp refinement
Dear all,
I'm trying to refine a structure using TLS on some of the domains
without refining the isotropic B factors of the atoms of the full
structure. I haven't been able to do this: the isotropic B factors
seem to be refined per residue when I include TLS. If I don't use
TLS, the B factors are not refined. I've looked around in the
archives and browsed the manual without luck. Any suggestions would
be highly appreciated. I include the parameter file I've used.
</pre>
</blockquote>
<pre wrap=""><!---->
Quoting Pavel (since he's teaching a workshop): "phenix.refine always
writes out the total B-factors and not split them. The total B-factor
in phenix.refine is defined as: Utotal = Utls + Ulocal + Ucryst." So
the atomic B-factors in your structure are not being refined
individually, but they change anyway because the contribution of the
TLS refinement is included.
-Nat
</pre>
<blockquote type="cite">
<pre wrap="">Kind regards,
Roeland Boer.
++++++++++++++ Parameters ++++++++++++++++
refinement.main.number_of_macro_cycles=4
refinement.main.ncs = True
refinement.input.xray_data {
labels=F
low_resolution=20.0
high_resolution=3.6
}
refinement.refine {
strategy=tls+individual_sites
adp {
tls="chain A and (resid 4:132 or resid 301)"
tls="chain B and (resid 4:132 or resid 301)"
tls="chain C and (resid 4:132 or resid 301)"
tls="chain X and (resid 4:132 or resid 301)"
tls="chain Y and (resid 4:132 or resid 301)"
tls="chain Z and (resid 4:132 or resid 301)"
}
}
refinement.ncs {
find_automatically = False
restraint_group {
reference = chain A and resid 133:203
selection = chain B and resid 133:203
selection = chain C and resid 133:203
selection = chain X and resid 133:203
selection = chain Y and resid 133:203
selection = chain Z and resid 133:203
}
restraint_group {
reference = chain B and (resid 4:132 or resid 301)
selection = chain A and (resid 4:132 or resid 301)
selection = chain C and (resid 4:132 or resid 301)
selection = chain X and (resid 4:132 or resid 301)
selection = chain Y and (resid 4:132 or resid 301)
selection = chain Z and (resid 4:132 or resid 301)
}
}
refinement.output.prefix=3.6-tlsnter-indsite-inputb-autowght-ncs
-------------------- Parameters --------------------------
</pre>
</blockquote>
<pre wrap=""><!---->
-------------------
Nathaniel Echols
Lawrence Berkeley Lab
510-486-5136
<a class="moz-txt-link-abbreviated" href="mailto:NEchols@lbl.gov">NEchols@lbl.gov</a>
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</pre>
</blockquote>
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