https://wiki.uni-konstanz.de/ccp4/index.php?title=Data_quality&feed=atom&action=history Data quality - Revision history 2024-03-28T16:01:59Z Revision history for this page on the wiki MediaWiki 1.39.6 https://wiki.uni-konstanz.de/ccp4/index.php?title=Data_quality&diff=860&oldid=prev Kay: /* Improved indicators for data quality */ 2008-05-09T15:11:10Z <p><span dir="auto"><span class="autocomment">Improved indicators for data quality</span></span></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:11, 9 May 2008</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l21">Line 21:</td> <td colspan="2" class="diff-lineno">Line 21:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* it depends on the multiplicity (unfortunately often called redundancy): the higher the multiplicity, the higher R&lt;sub&gt;merge&lt;/sub&gt; becomes</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* it depends on the multiplicity (unfortunately often called redundancy): the higher the multiplicity, the higher R&lt;sub&gt;merge&lt;/sub&gt; becomes</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* it assesses data consistency, not the quality of the reduced data</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* it assesses data consistency, not the quality of the reduced data</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>This has been discussed by Diederichs and Karplus&lt;ref name=&quot;DiKa97&quot;&gt;K. Diederichs and P.A. Karplus (1997). Improved R-factors for diffraction data analysis in macromolecular crystallography. Nature Struct. Biol. 4, 269-275 [http://strucbio.biologie.uni-konstanz.de/strucbio/files/nsb-1997.pdf]&lt;/ref&gt;<del style="font-weight: bold; text-decoration: none;">)</del>, who suggest a multiplicity-independant version called R&lt;sub&gt;meas&lt;/sub&gt;, which unfortunately is not used by everyone because the formula gives higher values than R&lt;sub&gt;merge&lt;/sub&gt;. R-factors for data quality assessment were also suggested by Diederichs and Karplus, and Weiss and Hilgenfeld &lt;ref name=&quot;WeHi97&quot;&gt;M.S. Weiss and R. Hilgenfeld (1997) On the use of the merging R-factor as a quality indicator for X-ray data. J. Appl. Crystallogr. 30, 203-205 [http://dx.doi.org/10.1107/S0021889897003907]&lt;/ref&gt;. Weiss &lt;ref name=&quot;We01&quot;&gt;M.S. Weiss (2001) Global indicators of X-ray data quality. J. Appl. Cryst. 34, 130-135 [http://dx.doi.org/10.1107/S0021889800018227]&lt;/ref&gt; showed that these R-factors are indeed strongly correlated with the quality of the data.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>This has been discussed by Diederichs and Karplus&lt;ref name=&quot;DiKa97&quot;&gt;K. Diederichs and P.A. Karplus (1997). Improved R-factors for diffraction data analysis in macromolecular crystallography. Nature Struct. Biol. 4, 269-275 [http://strucbio.biologie.uni-konstanz.de/strucbio/files/nsb-1997.pdf]&lt;/ref&gt;, who suggest a multiplicity-independant version called R&lt;sub&gt;meas&lt;/sub&gt;, which unfortunately is not used by everyone because the formula gives higher values than R&lt;sub&gt;merge&lt;/sub&gt;. R-factors for data quality assessment were also suggested by Diederichs and Karplus, and Weiss and Hilgenfeld &lt;ref name=&quot;WeHi97&quot;&gt;M.S. Weiss and R. Hilgenfeld (1997) On the use of the merging R-factor as a quality indicator for X-ray data. J. Appl. Crystallogr. 30, 203-205 [http://dx.doi.org/10.1107/S0021889897003907]&lt;/ref&gt;. Weiss &lt;ref name=&quot;We01&quot;&gt;M.S. Weiss (2001) Global indicators of X-ray data quality. J. Appl. Cryst. 34, 130-135 [http://dx.doi.org/10.1107/S0021889800018227]&lt;/ref&gt; showed that these R-factors are indeed strongly correlated with the quality of the data.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== References ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== References ==</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;references/&gt;</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;references/&gt;</div></td></tr> </table> Kay https://wiki.uni-konstanz.de/ccp4/index.php?title=Data_quality&diff=859&oldid=prev Kay at 15:10, 9 May 2008 2008-05-09T15:10:19Z <p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:10, 9 May 2008</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l5">Line 5:</td> <td colspan="2" class="diff-lineno">Line 5:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>This limit is commonly based on average &lt;math&gt;I/\sigma&lt;/math&gt;.  Examples of such choices are:</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>This limit is commonly based on average &lt;math&gt;I/\sigma&lt;/math&gt;.  Examples of such choices are:</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* &lt;math>I/\sigma=1&lt;/math> in the highest resolution shell</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* &lt;math>I/\sigma=2&lt;/math> in the highest resolution shell</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* at least 50% of reflections in the highest resolution shell have &lt;math>I/\sigma&lt;/math> > 2</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* ...</ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">- &lt;math&gt;I/\sigma=1&lt;/math&gt; </del>in the <del style="font-weight: bold; text-decoration: none;">highest resolution shell</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Some of these choices are more liberal than others (and so will result </ins>in <ins style="font-weight: bold; text-decoration: none;">higher resolution values).  It is probably not worthwhile to argue which choice is </ins>the <ins style="font-weight: bold; text-decoration: none;">best, since it is indeed a matter of personal preference.  </ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">- </del>&lt;<del style="font-weight: bold; text-decoration: none;">math</del>&gt;<del style="font-weight: bold; text-decoration: none;">I</del>/<del style="font-weight: bold; text-decoration: none;">\sigma=2</del>&lt;/<del style="font-weight: bold; text-decoration: none;">math</del>&gt; in the <del style="font-weight: bold; text-decoration: none;">highest resolution shell</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">There is probably not much reason to limit resolution by R</ins>&lt;<ins style="font-weight: bold; text-decoration: none;">sub</ins>&gt;<ins style="font-weight: bold; text-decoration: none;">merge&lt;</ins>/<ins style="font-weight: bold; text-decoration: none;">sub&gt;.  When the resolution limit is selected based on R&lt;sub&gt;merge</ins>&lt;/<ins style="font-weight: bold; text-decoration: none;">sub</ins>&gt; <ins style="font-weight: bold; text-decoration: none;">being less than a certain cutoff, the argument is that </ins>in <ins style="font-weight: bold; text-decoration: none;">higher resolution shells the variation among independent measurements of the intensity of </ins>the <ins style="font-weight: bold; text-decoration: none;">same reflection is too high.  But such variation is indeed bound to be high for weak reflections.  R&lt;sub&gt;merge&lt;/sub&gt; may and should be used as the measure of the overall data consistency (e.g. of two independent datasets the one that has higher R&lt;sub&gt;merge&lt;/sub&gt; probably is noisier).</ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>- <del style="font-weight: bold; text-decoration: none;">at least 50% of reflections </del>in the <del style="font-weight: bold; text-decoration: none;">highest </del>resolution <del style="font-weight: bold; text-decoration: none;">shell have </del>&lt;<del style="font-weight: bold; text-decoration: none;">math</del>&gt;<del style="font-weight: bold; text-decoration: none;">I/\sigma</del>&lt;/<del style="font-weight: bold; text-decoration: none;">math</del>&gt; <del style="font-weight: bold; text-decoration: none;">&gt; 2</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Of course you can achieve lower R</ins>-<ins style="font-weight: bold; text-decoration: none;">factors </ins>in <ins style="font-weight: bold; text-decoration: none;">refinement by setting </ins>the resolution <ins style="font-weight: bold; text-decoration: none;">limit based on some cutoff value of R</ins>&lt;<ins style="font-weight: bold; text-decoration: none;">sub</ins>&gt;<ins style="font-weight: bold; text-decoration: none;">merge</ins>&lt;/<ins style="font-weight: bold; text-decoration: none;">sub</ins>&gt;<ins style="font-weight: bold; text-decoration: none;">. It is perfectly OK to aspire low R-factors, but to achieve this by throwing away good data isn&#039;t. The better strategy probably is to choose a generous high resolution limit early during structure solution, and to decide near the end of the refinement, by inspecting maps and comparing model R-factors at different resolutions, at which resolution the useful signal vanishes in the noise.  </ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">...</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">== Improved indicators for data quality ==</ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Some of these choices are more liberal than others (and so will give you higher resolution).  It is probably not worthwhile to argue which choice is the best, since it is indeed a matter of personal preference.  </del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>R&lt;sub&gt;merge&lt;/sub&gt; is the wrong <ins style="font-weight: bold; text-decoration: none;">quantity </ins>to look at altogether, because  </div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">There is not probably much reason to limit resolution by R&lt;sub&gt;merge&lt;/sub&gt;.  When the resolution limit is selected based on R&lt;sub&gt;merge&lt;/sub&gt; being less than certain cutoff, the argument is that in higher resolution shells the variation among independent measurements of the intensity of the same reflection is too high.  But such variation is bound to be high for weak reflections.  Plus, factors such as redundancy may significantly affect R&lt;sub&gt;merge&lt;/sub&gt;.  R&lt;sub&gt;merge&lt;/sub&gt; may and should be used as the measure of the overall data quality (e.g. of two independent datasets the one that has higher R&lt;sub&gt;merge&lt;/sub&gt; probably is noisier).</del></div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">One thing you achieve by choosing resolution limit based on R&lt;sub&gt;merge&lt;/sub&gt; (which generally means that your &lt;math&gt;I/\sigma&lt;/math&gt; in the highest resolution shell will be &gt;4), of course, is lower R-factors in refinement.  It is perfectly OK to aspire low R-factors, but to achieve this by throwing away data probably isn&#039;t.</del></div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">== R&lt;sub&gt;merge&lt;/sub&gt; criticism ==</del></div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Finally, </del>R&lt;sub&gt;merge&lt;/sub&gt; is the wrong <del style="font-weight: bold; text-decoration: none;">quantitiy </del>to look at altogether, because  </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* it depends on the multiplicity (unfortunately often called redundancy): the higher the multiplicity, the higher R&lt;sub&gt;merge&lt;/sub&gt; becomes</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* it depends on the multiplicity (unfortunately often called redundancy): the higher the multiplicity, the higher R&lt;sub&gt;merge&lt;/sub&gt; becomes</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* it assesses data consistency, not the quality of the reduced data</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* it assesses data consistency, not the quality of the reduced data</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>This has been discussed by Diederichs and Karplus<del style="font-weight: bold; text-decoration: none;">(</del>&lt;ref name=&quot;DiKa97&quot;&gt;K. Diederichs and P.A. Karplus (1997). Improved R-factors for diffraction data analysis in macromolecular crystallography. Nature Struct. Biol. 4, 269-275 [http://strucbio.biologie.uni-konstanz.de/strucbio/files/nsb-1997.pdf]&lt;/ref&gt;), who suggest a multiplicity-independant version called R&lt;sub&gt;meas&lt;/sub&gt;, which unfortunately is not used by everyone because the formula gives higher values than R&lt;sub&gt;merge&lt;/sub&gt;. R-factors for data quality assessment were also suggested by Diederichs and Karplus, and Weiss and Hilgenfeld &lt;ref name=&quot;WeHi97&quot;&gt;M.S. Weiss and R. Hilgenfeld (1997) On the use of the merging R-factor as a quality indicator for X-ray data. J. Appl. Crystallogr. 30, 203-205[http://dx.doi.org/10.1107/S0021889897003907]&lt;/ref&gt;. Weiss &lt;ref name=&quot;We01&quot;&gt;M.S. Weiss<del style="font-weight: bold; text-decoration: none;">. </del>Global indicators of X-ray data quality. J. Appl. Cryst<del style="font-weight: bold; text-decoration: none;">. (2001)</del>. 34, 130-135 [http://dx.doi.org/10.1107/S0021889800018227]&lt;/ref&gt; showed that these R-factors are indeed strongly correlated with the quality of the data.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>This has been discussed by Diederichs and Karplus&lt;ref name=&quot;DiKa97&quot;&gt;K. Diederichs and P.A. Karplus (1997). Improved R-factors for diffraction data analysis in macromolecular crystallography. Nature Struct. Biol. 4, 269-275 [http://strucbio.biologie.uni-konstanz.de/strucbio/files/nsb-1997.pdf]&lt;/ref&gt;), who suggest a multiplicity-independant version called R&lt;sub&gt;meas&lt;/sub&gt;, which unfortunately is not used by everyone because the formula gives higher values than R&lt;sub&gt;merge&lt;/sub&gt;. R-factors for data quality assessment were also suggested by Diederichs and Karplus, and Weiss and Hilgenfeld &lt;ref name=&quot;WeHi97&quot;&gt;M.S. Weiss and R. Hilgenfeld (1997) On the use of the merging R-factor as a quality indicator for X-ray data. J. Appl. Crystallogr. 30, 203-205 [http://dx.doi.org/10.1107/S0021889897003907]&lt;/ref&gt;. Weiss &lt;ref name=&quot;We01&quot;&gt;M.S. Weiss <ins style="font-weight: bold; text-decoration: none;">(2001) </ins>Global indicators of X-ray data quality. J. Appl. Cryst. 34, 130-135 [http://dx.doi.org/10.1107/S0021889800018227]&lt;/ref&gt; showed that these R-factors are indeed strongly correlated with the quality of the data.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== References ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== References ==</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;references/&gt;</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;references/&gt;</div></td></tr> </table> Kay https://wiki.uni-konstanz.de/ccp4/index.php?title=Data_quality&diff=858&oldid=prev Kay at 14:52, 9 May 2008 2008-05-09T14:52:51Z <p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:52, 9 May 2008</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l25">Line 25:</td> <td colspan="2" class="diff-lineno">Line 25:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* it depends on the multiplicity (unfortunately often called redundancy): the higher the multiplicity, the higher R&lt;sub&gt;merge&lt;/sub&gt; becomes</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* it depends on the multiplicity (unfortunately often called redundancy): the higher the multiplicity, the higher R&lt;sub&gt;merge&lt;/sub&gt; becomes</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* it assesses data consistency, not the quality of the reduced data</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* it assesses data consistency, not the quality of the reduced data</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>This has been discussed by Diederichs and Karplus(&lt;ref name=&quot;DiKa97&quot;&gt;K. Diederichs and P.A. Karplus (1997). Improved R-factors for diffraction data analysis in macromolecular crystallography. Nature Struct. Biol. 4, 269-275 [http://strucbio.biologie.uni-konstanz.de/strucbio/files/nsb-1997.pdf]&lt;/ref&gt;), who suggest a multiplicity-independant version called R&lt;sub&gt;meas&lt;/sub&gt;, which unfortunately is not used by everyone because the formula gives higher values than R&lt;sub&gt;merge&lt;/sub&gt;. R-factors for data quality assessment were also suggested by Diederichs and Karplus, and Weiss and Hilgenfeld &lt;ref name=&quot;WeHi97&quot;&gt;M.S. Weiss and R. Hilgenfeld (1997) On the use of the merging R-factor as a quality indicator for X-ray data. J. Appl. Crystallogr. 30, 203-205[http://dx.doi.org/10.1107/S0021889897003907]&lt;/ref&gt;)</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>This has been discussed by Diederichs and Karplus(&lt;ref name=&quot;DiKa97&quot;&gt;K. Diederichs and P.A. Karplus (1997). Improved R-factors for diffraction data analysis in macromolecular crystallography. Nature Struct. Biol. 4, 269-275 [http://strucbio.biologie.uni-konstanz.de/strucbio/files/nsb-1997.pdf]&lt;/ref&gt;), who suggest a multiplicity-independant version called R&lt;sub&gt;meas&lt;/sub&gt;, which unfortunately is not used by everyone because the formula gives higher values than R&lt;sub&gt;merge&lt;/sub&gt;. R-factors for data quality assessment were also suggested by Diederichs and Karplus, and Weiss and Hilgenfeld &lt;ref name=&quot;WeHi97&quot;&gt;M.S. Weiss and R. Hilgenfeld (1997) On the use of the merging R-factor as a quality indicator for X-ray data. J. Appl. Crystallogr. 30, 203-205[http://dx.doi.org/10.1107/S0021889897003907]&lt;/ref&gt;<ins style="font-weight: bold; text-decoration: none;">. Weiss &lt;ref name=&quot;We01&quot;&gt;M.S. Weiss. Global indicators of X-ray data quality. J. Appl. Cryst. (2001</ins>)<ins style="font-weight: bold; text-decoration: none;">. 34, 130-135 [http://dx.doi.org/10.1107/S0021889800018227]&lt;/ref&gt; showed that these R-factors are indeed strongly correlated with the quality of the data.</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">== References ==</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">&lt;references/&gt;</ins></div></td></tr> </table> Kay https://wiki.uni-konstanz.de/ccp4/index.php?title=Data_quality&diff=857&oldid=prev Kay: Rmerge subscripts 2008-05-09T14:49:27Z <p>Rmerge subscripts</p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:49, 9 May 2008</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l16">Line 16:</td> <td colspan="2" class="diff-lineno">Line 16:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Some of these choices are more liberal than others (and so will give you higher resolution).  It is probably not worthwhile to argue which choice is the best, since it is indeed a matter of personal preference.   </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Some of these choices are more liberal than others (and so will give you higher resolution).  It is probably not worthwhile to argue which choice is the best, since it is indeed a matter of personal preference.   </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>There is not probably much reason to limit resolution by <del style="font-weight: bold; text-decoration: none;">Rmerge</del>.  When the resolution limit is selected based on <del style="font-weight: bold; text-decoration: none;">Rmerge </del>being less than certain cutoff, the argument is that in higher resolution shells the variation among independent measurements of the intensity of the same reflection is too high.  But such variation is bound to be high for weak reflections.  Plus, factors such as redundancy may significantly affect <del style="font-weight: bold; text-decoration: none;">Rmerge</del>.  <del style="font-weight: bold; text-decoration: none;">Rmerge </del>may and should be used as the measure of the overall data quality (e.g. of two independent datasets the one that has higher <del style="font-weight: bold; text-decoration: none;">Rmerge </del>probably is noisier).</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>There is not probably much reason to limit resolution by <ins style="font-weight: bold; text-decoration: none;">R&lt;sub&gt;merge&lt;/sub&gt;</ins>.  When the resolution limit is selected based on <ins style="font-weight: bold; text-decoration: none;">R&lt;sub&gt;merge&lt;/sub&gt; </ins>being less than certain cutoff, the argument is that in higher resolution shells the variation among independent measurements of the intensity of the same reflection is too high.  But such variation is bound to be high for weak reflections.  Plus, factors such as redundancy may significantly affect <ins style="font-weight: bold; text-decoration: none;">R&lt;sub&gt;merge&lt;/sub&gt;</ins>.  <ins style="font-weight: bold; text-decoration: none;">R&lt;sub&gt;merge&lt;/sub&gt; </ins>may and should be used as the measure of the overall data quality (e.g. of two independent datasets the one that has higher <ins style="font-weight: bold; text-decoration: none;">R&lt;sub&gt;merge&lt;/sub&gt; </ins>probably is noisier).</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>One thing you achieve by choosing resolution limit based on <del style="font-weight: bold; text-decoration: none;">Rmerge </del>(which generally means that your &lt;math&gt;I/\sigma&lt;/math&gt; in the highest resolution shell will be &gt;4), of course, is lower R-factors in refinement.  It is perfectly OK to aspire low R-factors, but to achieve this by throwing away data probably isn&#039;t.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>One thing you achieve by choosing resolution limit based on <ins style="font-weight: bold; text-decoration: none;">R&lt;sub&gt;merge&lt;/sub&gt; </ins>(which generally means that your &lt;math&gt;I/\sigma&lt;/math&gt; in the highest resolution shell will be &gt;4), of course, is lower R-factors in refinement.  It is perfectly OK to aspire low R-factors, but to achieve this by throwing away data probably isn&#039;t.</div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">== R&lt;sub&gt;merge&lt;/sub&gt; criticism ==</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Finally, R&lt;sub&gt;merge&lt;/sub&gt; is the wrong quantitiy to look at altogether, because </ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* it depends on the multiplicity (unfortunately often called redundancy): the higher the multiplicity, the higher R&lt;sub&gt;merge&lt;/sub&gt; becomes</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* it assesses data consistency, not the quality of the reduced data</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">This has been discussed by Diederichs and Karplus(&lt;ref name=&quot;DiKa97&quot;&gt;K. Diederichs and P.A. Karplus (1997). Improved R-factors for diffraction data analysis in macromolecular crystallography. Nature Struct. Biol. 4, 269-275 [http://strucbio.biologie.uni-konstanz.de/strucbio/files/nsb-1997.pdf]&lt;/ref&gt;), who suggest a multiplicity-independant version called R&lt;sub&gt;meas&lt;/sub&gt;, which unfortunately is not used by everyone because the formula gives higher values than R&lt;sub&gt;merge&lt;/sub&gt;. R-factors for data quality assessment were also suggested by Diederichs and Karplus, and Weiss and Hilgenfeld &lt;ref name=&quot;WeHi97&quot;&gt;M.S. Weiss and R. Hilgenfeld (1997) On the use of the merging R-factor as a quality indicator for X-ray data. J. Appl. Crystallogr. 30, 203-205[http://dx.doi.org/10.1107/S0021889897003907]&lt;/ref&gt;)</ins></div></td></tr> </table> Kay https://wiki.uni-konstanz.de/ccp4/index.php?title=Data_quality&diff=205&oldid=prev Pozharski at 14:41, 11 February 2008 2008-02-11T14:41:14Z <p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:41, 11 February 2008</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l18">Line 18:</td> <td colspan="2" class="diff-lineno">Line 18:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There is not probably much reason to limit resolution by Rmerge.  When the resolution limit is selected based on Rmerge being less than certain cutoff, the argument is that in higher resolution shells the variation among independent measurements of the intensity of the same reflection is too high.  But such variation is bound to be high for weak reflections.  Plus, factors such as redundancy may significantly affect Rmerge.  Rmerge may and should be used as the measure of the overall data quality (e.g. of two independent datasets the one that has higher Rmerge probably is noisier).</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There is not probably much reason to limit resolution by Rmerge.  When the resolution limit is selected based on Rmerge being less than certain cutoff, the argument is that in higher resolution shells the variation among independent measurements of the intensity of the same reflection is too high.  But such variation is bound to be high for weak reflections.  Plus, factors such as redundancy may significantly affect Rmerge.  Rmerge may and should be used as the measure of the overall data quality (e.g. of two independent datasets the one that has higher Rmerge probably is noisier).</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>One thing you achieve by choosing resolution limit based on Rmerge (which generally means that your I/sigma in the highest resolution shell will be &gt;4), of course, is lower R-factors in refinement.  It is perfectly OK to aspire low R-factors, but to achieve this by throwing away data probably isn&#039;t.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>One thing you achieve by choosing resolution limit based on Rmerge (which generally means that your <ins style="font-weight: bold; text-decoration: none;">&lt;math&gt;</ins>I/<ins style="font-weight: bold; text-decoration: none;">\</ins>sigma<ins style="font-weight: bold; text-decoration: none;">&lt;/math&gt; </ins>in the highest resolution shell will be &gt;4), of course, is lower R-factors in refinement.  It is perfectly OK to aspire low R-factors, but to achieve this by throwing away data probably isn&#039;t.</div></td></tr> </table> Pozharski https://wiki.uni-konstanz.de/ccp4/index.php?title=Data_quality&diff=134&oldid=prev Wgscott: changed to greek letter sigma 2008-02-10T02:20:11Z <p>changed to greek letter sigma</p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 03:20, 10 February 2008</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l3">Line 3:</td> <td colspan="2" class="diff-lineno">Line 3:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>First of all, it is limited by completeness.  In practical terms this means that the highest resolution you can get is the resolution at the edge of the detector.  If you collected enough frames, you may be able to squeeze out 0.1A if you process data all the way to the corner.  Usually the detector is positioned close enough to the crystal so that you don&#039;t have any diffraction at the edge and then resolution limits should be chosen based on strength of the diffraction.   </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>First of all, it is limited by completeness.  In practical terms this means that the highest resolution you can get is the resolution at the edge of the detector.  If you collected enough frames, you may be able to squeeze out 0.1A if you process data all the way to the corner.  Usually the detector is positioned close enough to the crystal so that you don&#039;t have any diffraction at the edge and then resolution limits should be chosen based on strength of the diffraction.   </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>This limit is commonly based on average I/sigma.  Examples of such choices are:</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>This limit is commonly based on average <ins style="font-weight: bold; text-decoration: none;">&lt;math&gt;</ins>I/<ins style="font-weight: bold; text-decoration: none;">\</ins>sigma<ins style="font-weight: bold; text-decoration: none;">&lt;/math&gt;</ins>.  Examples of such choices are:</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">- I/sigma=1 in the highest resolution shell</del></div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>- I/sigma=<del style="font-weight: bold; text-decoration: none;">2 </del>in the highest resolution shell</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>- <ins style="font-weight: bold; text-decoration: none;">&lt;math&gt;</ins>I/<ins style="font-weight: bold; text-decoration: none;">\</ins>sigma=<ins style="font-weight: bold; text-decoration: none;">1&lt;/math&gt; </ins>in the highest resolution shell</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>- at least 50% of reflections in the highest resolution shell have I/sigma&gt;2</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">- &lt;math&gt;I/\sigma=2&lt;/math&gt; in the highest resolution shell</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>- at least 50% of reflections in the highest resolution shell have <ins style="font-weight: bold; text-decoration: none;">&lt;math&gt;</ins>I/<ins style="font-weight: bold; text-decoration: none;">\</ins>sigma<ins style="font-weight: bold; text-decoration: none;">&lt;/math&gt; </ins>&gt; 2</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>...</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>...</div></td></tr> </table> Wgscott https://wiki.uni-konstanz.de/ccp4/index.php?title=Data_quality&diff=82&oldid=prev Pozharski: New page: == What is the resolution of my dataset? == First of all, it is limited by completeness. In practical terms this means that the highest resolution you can get is the resolution at the ed... 2008-02-09T05:44:03Z <p>New page: == What is the resolution of my dataset? == First of all, it is limited by completeness. In practical terms this means that the highest resolution you can get is the resolution at the ed...</p> <p><b>New page</b></p><div>== What is the resolution of my dataset? ==<br /> <br /> First of all, it is limited by completeness. In practical terms this means that the highest resolution you can get is the resolution at the edge of the detector. If you collected enough frames, you may be able to squeeze out 0.1A if you process data all the way to the corner. Usually the detector is positioned close enough to the crystal so that you don&#039;t have any diffraction at the edge and then resolution limits should be chosen based on strength of the diffraction. <br /> <br /> This limit is commonly based on average I/sigma. Examples of such choices are:<br /> <br /> - I/sigma=1 in the highest resolution shell<br /> <br /> - I/sigma=2 in the highest resolution shell<br /> <br /> - at least 50% of reflections in the highest resolution shell have I/sigma&gt;2<br /> <br /> ...<br /> <br /> Some of these choices are more liberal than others (and so will give you higher resolution). It is probably not worthwhile to argue which choice is the best, since it is indeed a matter of personal preference. <br /> <br /> There is not probably much reason to limit resolution by Rmerge. When the resolution limit is selected based on Rmerge being less than certain cutoff, the argument is that in higher resolution shells the variation among independent measurements of the intensity of the same reflection is too high. But such variation is bound to be high for weak reflections. Plus, factors such as redundancy may significantly affect Rmerge. Rmerge may and should be used as the measure of the overall data quality (e.g. of two independent datasets the one that has higher Rmerge probably is noisier).<br /> <br /> One thing you achieve by choosing resolution limit based on Rmerge (which generally means that your I/sigma in the highest resolution shell will be &gt;4), of course, is lower R-factors in refinement. It is perfectly OK to aspire low R-factors, but to achieve this by throwing away data probably isn&#039;t.</div> Pozharski