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Dear Toon, <br>
<br>
if you have data up to 2.3A resolution, you should keep it, it is so
valuable. The isotropic statistics that you are looking at and
output by Aimless are I'm sure awful, because you simply don't have
data (lack of completeness) in the high resolution shells, and the
statistics are produced out of a mixture of real data (weak) and
noise. <br>
<br>
Staraniso has done a lot of work on outputting statistics more
meaningful in term of Table 1 and anisotropy, so it could be worth a
try to submit your data and see what comes out of it. <br>
In any case, I would use the data to the resolution limit suggested
by Aimless, and judge your electron density maps. I'm sure you will
have a big improvement if you include the 2.3A limit, even though it
is not going to look like an isotropic 2.3A. <br>
<br>
If you use the data output by staraniso, please ask the server to
also output your original data so you can deposit the original
intensities in the PDB and investigators can look at it untouched in
the future. There is a check box on the server to tick. <br>
<br>
Best of luck with your data<br>
Vincent<br>
<br>
<div class="moz-cite-prefix">On 04/04/2018 11:47, Toon Van Thillo
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:1522835276615.28480@student.kuleuven.be">
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<p>Hi all,<br>
</p>
<p><br>
</p>
<p>Currently I am refining a data set which showed anisotropic
diffraction. Aimless suggested cutoffs at 2.3, 2.6 and 3.6
angstrom for the h,k and l axis.<br>
</p>
<p>I chose a general 3.6 cutoff to obtain satisfactory statistics
for Rmeas, I/sd(I) and CC1/2. At this resolution the data set
consists of approximately 2800 reflections.<br>
</p>
<p><br>
</p>
<p>Generally 5% of the set is set aside as the Rfree test set and
I found that a minimum of 500 reflections in total is used to
produce a reliable Rfree. However, 5% only amounts to 140
reflections in this case. I am hesitant to include more
reflections as I would have to go up to 20% of the reflections
to obtain more than 500 reflections for the test set. In a
discussion on the CCP4 message boards some time ago it was
suggested to do multiple refinements with different test sets:<br>
</p>
<p><a
href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1411&L=ccp4bb&F=&S=&P=125570"
moz-do-not-send="true">https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1411&L=ccp4bb&F=&S=&P=125570</a><br>
</p>
<p><br>
</p>
<p>In the thread it was also discussed that a least squares
approach is prefered when using a small test set. However, when
using a LS target, the resulting Rfree is very high (10% higher
than when using the automatic option) and <em>phenix.refine</em>
produces awful geometry (24% ramachandran outliers, 105
clashcore...). It seems that the refinement is performed without
restraints? Optimize X-ray/stereochemistry weight does not
result in improved stereochemistry. My question is if the LS
approach is still relevant and if so, is there an explanation
(and solution) for the bad statistics?<br>
</p>
<p><br>
</p>
<p>Kind regards,<br>
</p>
<p><br>
</p>
<p>Toon Van Thillo<br>
</p>
<p><br>
</p>
<p><br>
</p>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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<p class="p1"><span class="s1">Vincent Chaptal, PhD</span></p>
<p class="p1"><span class="s1">Institut de Biologie et Chimie des
Protéines</span></p>
<p class="p1"><span class="s1">Drug Resistance and Membrane
Proteins Laboratory</span></p>
<p class="p1"><span class="s1">7 passage du Vercors<span
class="Apple-converted-space"> </span></span></p>
<p class="p1"><span class="s1">69007 LYON</span></p>
<p class="p1"><span class="s1">FRANCE</span></p>
<p class="p1"><span class="s1">+33 4 37 65 29 01</span></p>
<p class="p1"><span class="s1"><a class="moz-txt-link-freetext" href="http://www.ibcp.fr">http://www.ibcp.fr</a></span></p>
<p class="p1"><span class="s1"><br>
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