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<div class="moz-cite-prefix">Hi Ursula,<br>
<br>
here is a solution, not nice though:<br>
<br>
step 1: get a pdb file with chain in question:<br>
<br>
phenix.pdbtools model.pdb keep="chain A"
output.file_name="chain_A.pdb"<br>
<br>
step 2: then this will give you average B<br>
<br>
phenix.pdbtools chain_A.pdb model_statistics=true<br>
<br>
Other suggestions (by David & Christian) might work too, but I
have no idea how these programs handle TLS contribution to ADP and
ANISOU records. Though since phenix.refine outputs total ADPs I
guess this should be just fine.<br>
<br>
Pavel<br>
<br>
On 7/12/12 9:24 AM, Ursula Schulze-Gahmen wrote:<br>
</div>
<blockquote
cite="mid:CA+erM+1nNV3sX1it_j93pTnbGj9YM58sTRy7HRBgEBPXyKYf8g@mail.gmail.com"
type="cite">Hi Pavel,<br>
<br>
Yes, I see the baverage in the header of the pdb file. But I would
like to get the baverage for the different chains in the
structure. I tried using "phenix.pdbtools model.pdb
model_statistics=true" on separate chains, but I don't get a value
for Baverage from this.<br>
<br>
Ursula<br>
<br>
<div class="gmail_quote">On Wed, Jul 11, 2012 at 11:58 AM, Pavel
Afonine <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Ursula,
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Is there an easy way to calculate average temperature
factors in phenix or another program after ADP + TLS
refinement in phenix?<br>
</blockquote>
<br>
</div>
yes. If you PDB file is after phenix.refine run, then the
average ADP is reported in PDB file header as well as in
refinement log file.<br>
For a PDB file you can calculate average ADP using this
command:<br>
<br>
phenix.pdbtools model.pdb model_statistics=true<br>
<br>
It does not matter where PDB file come from as long as ATOM
or/and ANISOU records contain the correct ADPs.<br>
<br>
Pavel<br>
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</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Ursula Schulze-Gahmen, Ph.D.<br>
Assistant Researcher<br>
UC Berkeley, QB3<br>
356 Stanley Hall #3220<br>
Berkeley, CA 94720-3220<br>
<br>
<br>
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</blockquote>
<br>
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