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Hi,<br>
<br>
I realized Randy's reply did not go to the mailing list, so I'm
forwarding it now.<br>
<br>
Pavel<br>
<br>
<br>
-------- Original Message --------
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Subject: </th>
<td>Re: [phenixbb] anisotropic induced noise amplification</td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Date: </th>
<td>Mon, 7 May 2012 09:49:57 +0100</td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">From: </th>
<td>Randy Read <a class="moz-txt-link-rfc2396E" href="mailto:rjr27@cam.ac.uk"><rjr27@cam.ac.uk></a></td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">To: </th>
<td>Pavel Afonine <a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a></td>
</tr>
<tr>
<th align="RIGHT" nowrap="nowrap" valign="BASELINE">CC: </th>
<td><a class="moz-txt-link-abbreviated" href="mailto:developers@phenix-online.org">developers@phenix-online.org</a>
<a class="moz-txt-link-rfc2396E" href="mailto:developers@phenix-online.org"><developers@phenix-online.org></a>, Peter Zwart
<a class="moz-txt-link-rfc2396E" href="mailto:PHZwart@lbl.gov"><PHZwart@lbl.gov></a></td>
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<br>
<br>
In the absence of an answer from Peter (who implemented this and
therefore ought to know best), I'm pretty sure that the idea is to
measure how much difference there is in the amount of signal in the
data that have received the biggest anisotropy corrections, compared
to the ones that have received the smallest anisotropy corrections.
If there's very little signal in the data that have been scaled up
the most, then the noise is being amplified (nearly-random
amplitudes have gone from being relatively small to the same size on
average as the well-measured amplitudes).
<div><br>
</div>
<div>
<div>But what the Z-scores mean is not at all clear from that
output, and I'm not aware that Peter has written anything
describing this.</div>
<div><br>
</div>
This amplified noise is what I suspect is creating problems in
phenix.refine refinement with highly anisotropic data, because if
the experimental sigmas are ignored then the program doesn't know
(after anisotropic scaling) which amplitudes of a comparable size
contain signal and which are essentially noise. Anisotropic
truncation gets rid of it, which would explain why refinement
works better with anisotropically-truncated data.<br>
<div><br>
</div>
<div>Randy</div>
<div><br>
<div>
<div>On 6 May 2012, at 20:21, Pavel Afonine wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
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charset=ISO-8859-1">
<div text="#000000" bgcolor="#FFFFFF"> Hi,<br>
<br>
did anyone address this post? I'm interested to know the
answer myself: I have absolutely no idea what is this. <br>
<br>
Pavel<br>
<br>
-------- Original Message --------
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Subject:
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<td>[phenixbb] anisotropic induced noise
amplification</td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Date:
</th>
<td>Wed, 2 May 2012 16:06:55 -0500</td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">From:
</th>
<td>James Thompson <a moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:Thompson.James@mayo.edu"><Thompson.James@mayo.edu></a></td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Reply-To:
</th>
<td>PHENIX user mailing list <a
moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a></td>
</tr>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">To:
</th>
<td><a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></td>
</tr>
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<br>
<br>
<span class="Apple-style-span" style="font-size: 18px; ">Anyone
willing to summarize Xtriage's algorithm that determines
whether "<i>anisotropic induced noise amplification</i>"
is present in diffraction data? What is this noise
amplification? Is it anisotropic correction factors
that over-fit the data thereby inducing noise?</span>
<div style="font-size: 18px; "><br>
</div>
<div style="font-size: 18px; ">Many thanks,</div>
<div><span class="Apple-style-span" style="font-size:
18px; ">Jim T</span><br style="font-size: 18px; ">
<div style="font-size: 18px; "><br>
</div>
<div style="font-size: 18px; ">
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
">---------------- Anisotropy analyses
----------------</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; min-height: 13px;
font-size: 16px; "><br>
</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
">Anisotropy ( [MaxAnisoB-MinAnisoB]/[MaxAnisoB]
) : 3.596e-01</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
"> Anisotropic ratio
p-value : 0.000e+00</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; min-height: 13px;
font-size: 16px; "><br>
</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
"> The p-value is a measure of the severity of
anisotropy as observed in the PDB.</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
"> The p-value of 0.000e+00 indicates that
roughly 100.0 % of datasets available in the PDB
have</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
"> an anisotropy equal to or worse than this
dataset.</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; min-height: 13px;
font-size: 16px; "><br>
</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; min-height: 13px;
font-size: 16px; "><br>
</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
">For the resolution shell spanning between 2.36 -
2.20 Angstrom,</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
">the mean I/sigI is equal to 3.37. 42.2 % of these
intensities have</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
">an I/sigI > 3. When sorting these intensities
by their anisotropic</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
">correction factor and analysing the I/sigI
behavior for this ordered</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
">list, we can gauge the presence of 'anisotropy
induced noise amplification'</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
">in reciprocal space.</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; min-height: 13px;
font-size: 16px; "><br>
</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
"> The quarter of Intensities *least* affected by
the anisotropy correction show</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
"> <I/sigI> : 3.82e+00</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
"> Fraction of I/sigI > 3 : 5.01e-01 (
Z = 3.59 )</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; min-height: 13px;
font-size: 16px; "><br>
</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
"> The quarter of Intensities *most* affected by
the anisotropy correction show</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
"> <I/sigI> : 2.02e+00</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 16px;
"> Fraction of I/sigI > 3 : 1.84e-01 (
Z = 10.78 )</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; min-height: 13px;
font-size: 16px; "><br>
</div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 18px;
"><b>The combined Z-score of 11.36 indicates that
there probably is significant</b></div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 18px;
"><b>systematic noise amplification that could
possibly lead to artefacts in the</b></div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px; font: normal
normal normal 11px/normal Courier; font-size: 18px;
"><b>maps or difficulties in refinement</b></div>
</div>
<div><br>
</div>
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</div>
<span><Attached Message Part.txt></span></blockquote>
</div>
<br>
<div>
<span class="Apple-style-span" style="border-collapse:
separate; color: rgb(0, 0, 0); font-family: Helvetica;
font-size: 12px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: auto; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-border-horizontal-spacing: 0px;
-webkit-border-vertical-spacing: 0px;
-webkit-text-decorations-in-effect: none;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width:
0; "><span class="Apple-style-span" style="border-collapse:
separate; color: rgb(0, 0, 0); font-family: Helvetica;
font-size: 12px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-indent: 0px; text-transform:
none; white-space: normal; widows: 2; word-spacing: 0px;
-webkit-border-horizontal-spacing: 0px;
-webkit-border-vertical-spacing: 0px;
-webkit-text-decorations-in-effect: none;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width:
0px; ">
<div>------</div>
<div>Randy J. Read</div>
<div>Department of Haematology, University of Cambridge</div>
<div>Cambridge Institute for Medical Research Tel: +
44 1223 336500</div>
<div>Wellcome Trust/MRC Building Fax: +
44 1223 336827</div>
<div>Hills Road E-mail:
<a moz-do-not-send="true" href="mailto:rjr27@cam.ac.uk">rjr27@cam.ac.uk</a></div>
<div>Cambridge CB2 0XY, U.K.
www-structmed.cimr.cam.ac.uk</div>
</span></span>
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