Hi,<br>I was trying to get one ADP per residue using the command as suggested in the PHENIX document:<br><br><p class="first"><strong>Refining group isotropic B-factors</strong>
</p><p class="first">One B-factor per residue:
</p><pre class="literal-block">% phenix.refine data.hkl model.pdb strategy=group_adp<br><br><br>See a part of my out pdb file (column 11):<br><br>ATOM 6971 C2 ADE F 15 -29.960 -20.547 -31.167 1.00 23.82 F C<br>
ATOM 6972 N1 ADE F 15 -30.382 -20.054 -32.336 1.00 24.20 F N<br>ATOM 6973 C6 ADE F 15 -30.077 -20.702 -33.471 1.00 21.52 F C<br>ATOM 6974 N6 ADE F 15 -30.496 -20.192 -34.629 1.00 20.08 F N<br>
ATOM 6975 C5 ADE F 15 -29.321 -21.893 -33.361 1.00 21.08 F C<br>ATOM 6976 N7 ADE F 15 -28.823 -22.777 -34.307 1.00 22.85 F N<br>ATOM 6977 C8 ADE F 15 -28.193 -23.670 -33.593 1.00 21.80 F C<br>
ATOM 6978 C2' ADE F 15 -27.648 -25.781 -31.357 1.00 22.11 F C<br>�<br><br>But, I got different temperature factors for different atoms in the same residue. Is that what I should get? How can I create one <br>
temperature factor for each residue? <br><br>Regards...<br><br>Hena<br></pre><br><br><div class="gmail_quote">On Thu, May 26, 2011 at 11:05 AM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov">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;"><u></u>
<div bgcolor="#ffffff" text="#000000">
Hi Christian,<br>
<br>
the problem is that you did not ask phenix.refine to refine the rest
of the atoms isotropically (with your command below you only refine
anisotropic ADPs of atoms in chain Q, and the B-factors of all the
other atoms are not refined):<br>
<br>
<blockquote type="cite">
<div style="font-family:-moz-fixed;font-size:12px" lang="x-unicode">
<pre> adp {
individual {
anisotropic = "chain Q"
}</pre>
</div>
</blockquote>
<br>
I would do it like this:<br>
<br>
adp {<br>
� individual {<br>
���� anisotropic = chain Q and element CL<br>
���� isotropic = not (chain Q and element CL)<br>
� }<br>
}<br>
<br>
Pavel.<br>
<br>
</div>
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<br></blockquote></div><br>