https://dictionary.iucr.org/index.php?title=Molecular_replacement&feed=atom&action=history
Molecular replacement - Revision history
2024-03-29T10:37:27Z
Revision history for this page on the wiki
MediaWiki 1.30.0
https://dictionary.iucr.org/index.php?title=Molecular_replacement&diff=4538&oldid=prev
BrianMcMahon: Added German and Spanish translations (U. Mueller)
2017-11-16T13:01:52Z
<p>Added German and Spanish translations (U. Mueller)</p>
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<td colspan="2" style="background-color: white; color:black; text-align: center;">Revision as of 13:01, 16 November 2017</td>
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<tr><td class='diff-marker'>−</td><td style="color:black; 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 class="diffchange diffchange-inline">Font </del>color="blue">Méthode du remplacement moléculaire</<del class="diffchange diffchange-inline">Font</del>> (''Fr''). <<del class="diffchange diffchange-inline">Font </del>color="black"> Metodo della sostituzione molecolare</<del class="diffchange diffchange-inline">Font</del>> (''It''). <<del class="diffchange diffchange-inline">Font </del>color="purple">分子置換法</<del class="diffchange diffchange-inline">Font</del>> (''Ja'').  </div></td><td class='diff-marker'>+</td><td style="color:black; 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 class="diffchange diffchange-inline">font </ins>color="blue">Méthode du remplacement moléculaire</<ins class="diffchange diffchange-inline">font</ins>> (''Fr''). <<ins class="diffchange diffchange-inline">font color="red">Molekularer Ersatz</font> (''Ge''). <font </ins>color="black">Metodo della sostituzione molecolare</<ins class="diffchange diffchange-inline">font</ins>> (''It''). <<ins class="diffchange diffchange-inline">font </ins>color="purple">分子置換法</<ins class="diffchange diffchange-inline">font</ins>> (''Ja<ins class="diffchange diffchange-inline">''). <font color="green">Reemplazamiento molecular</font> (''Sp</ins>'').</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Definition ==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Definition ==</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== See also ==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== See also ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; 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>*[[Noncrystallographic symmetry]]<del class="diffchange diffchange-inline">. </del></div></td><td class='diff-marker'>+</td><td style="color:black; 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 class="diffchange diffchange-inline">* [[Isomorphous replacement]]</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; 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>*D. M. Blow. ''International Tables for Crystallography'' (2006). Vol. F, ch. 13.1, pp. 263-268  [http://dx.doi.org/10.1107/97809553602060000681 doi:10.1107/97809553602060000681]  </div></td><td class='diff-marker'>+</td><td style="color:black; 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>* [[Noncrystallographic symmetry]]</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; 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>* D. M. Blow. ''International Tables for Crystallography'' (2006). Vol. F, ch. 13.1, pp. 263-268  [http://dx.doi.org/10.1107/97809553602060000681 doi:10.1107/97809553602060000681]  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Biological crystallography]]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Biological crystallography]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Structure determination]]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Structure determination]]</div></td></tr>
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BrianMcMahon
https://dictionary.iucr.org/index.php?title=Molecular_replacement&diff=3621&oldid=prev
BrianMcMahon: "superimpose" in the figure caption changed to "superpose", since an exact coincidence of source and target is meant.
2015-08-13T10:31:31Z
<p>"superimpose" in the figure caption changed to "superpose", since an exact coincidence of source and target is meant.</p>
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<td colspan="2" style="background-color: white; color:black; text-align: center;">Revision as of 10:31, 13 August 2015</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The technique is most commonly used in biological crystallography. Typically, an attempt is made to fit the structure under investigation (the 'target' structure) to a previously solved ('probe') structure. The probe may be a different crystal form of the same protein; or it may be a different protein with a high level of sequence identity, which correlates well with structural resemblance. As a rule of thumb, molecular replacement is often straightforward if the probe is well characterised and shares at least 40% sequence identity with the target.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The technique is most commonly used in biological crystallography. Typically, an attempt is made to fit the structure under investigation (the 'target' structure) to a previously solved ('probe') structure. The probe may be a different crystal form of the same protein; or it may be a different protein with a high level of sequence identity, which correlates well with structural resemblance. As a rule of thumb, molecular replacement is often straightforward if the probe is well characterised and shares at least 40% sequence identity with the target.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; 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>[[Image:RTfunctioninMR.gif|frame|Figure 1. Illustration of the rotation and translation functions applied to <del class="diffchange diffchange-inline">superimpose </del>a probe and target structure in molecular replacement.|right]]</div></td><td class='diff-marker'>+</td><td style="color:black; 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>[[Image:RTfunctioninMR.gif|frame|Figure 1. Illustration of the rotation and translation functions applied to <ins class="diffchange diffchange-inline">superpose </ins>a probe and target structure in molecular replacement.|right]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Figure 1 illustrates schematically the process of repositioning the probe structure (the solid motif) in the new unit cell to coincide with the target structure (red outline motif). Rotation and transformation matrices must be applied. [[Patterson methods]] are suitable for determining the rotation function '''R''', since intramolecular vectors are all shifted to the origin of a Patterson map. The orientational fit (''i.e.'' the quality of the calculated rotation function) has usually been assessed by monitoring [[R factor|''R'' factors]] or [[real-space correlation coefficient]]s. Increasingly, modern programs use [[maximum likelihood]] based algorthms.  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Figure 1 illustrates schematically the process of repositioning the probe structure (the solid motif) in the new unit cell to coincide with the target structure (red outline motif). Rotation and transformation matrices must be applied. [[Patterson methods]] are suitable for determining the rotation function '''R''', since intramolecular vectors are all shifted to the origin of a Patterson map. The orientational fit (''i.e.'' the quality of the calculated rotation function) has usually been assessed by monitoring [[R factor|''R'' factors]] or [[real-space correlation coefficient]]s. Increasingly, modern programs use [[maximum likelihood]] based algorthms.  </div></td></tr>
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BrianMcMahon
https://dictionary.iucr.org/index.php?title=Molecular_replacement&diff=3552&oldid=prev
MassimoNespolo: lang
2015-03-20T14:27:06Z
<p>lang</p>
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<td colspan="2" style="background-color: white; color:black; text-align: center;">Revision as of 14:27, 20 March 2015</td>
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<tr><td class='diff-marker'>−</td><td style="color:black; 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><Font color="blue"> Méthode du remplacement moléculaire </Font> (''Fr''). <Font color=""> <del class="diffchange diffchange-inline">Méthode du remplacement moléculaire </del></Font> (''<del class="diffchange diffchange-inline">Fr</del>'').  </div></td><td class='diff-marker'>+</td><td style="color:black; 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><Font color="blue">Méthode du remplacement moléculaire</Font> (''Fr''). <Font color="<ins class="diffchange diffchange-inline">black</ins>"> <ins class="diffchange diffchange-inline">Metodo della sostituzione molecolare</ins></Font> (''<ins class="diffchange diffchange-inline">It''). <Font color="purple">分子置換法</Font> (''Ja</ins>'').  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Definition ==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Definition ==</div></td></tr>
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MassimoNespolo
https://dictionary.iucr.org/index.php?title=Molecular_replacement&diff=3551&oldid=prev
MassimoNespolo: bぁck
2015-03-20T14:25:45Z
<p>bぁck</p>
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<td colspan="2" style="background-color: white; color:black; text-align: center;">Revision as of 14:25, 20 March 2015</td>
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<tr><td class='diff-marker'>−</td><td style="color:black; 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><Font color="blue"> Méthode du remplacement moléculaire </Font> (''Fr'').  </div></td><td class='diff-marker'>+</td><td style="color:black; 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><Font color="blue<ins class="diffchange diffchange-inline">"> Méthode du remplacement moléculaire </Font> (''Fr''). <Font color="</ins>"> Méthode du remplacement moléculaire </Font> (''Fr'').  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Definition ==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Definition ==</div></td></tr>
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MassimoNespolo
https://dictionary.iucr.org/index.php?title=Molecular_replacement&diff=3530&oldid=prev
MassimoNespolo: /* See also */ link
2015-03-20T04:26:19Z
<p><span dir="auto"><span class="autocomment">See also: </span> link</span></p>
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<td colspan="2" style="background-color: white; color:black; text-align: center;">Revision as of 04:26, 20 March 2015</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== See also ==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== See also ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; 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>Noncrystallographic symmetry.</div></td><td class='diff-marker'>+</td><td style="color:black; 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 class="diffchange diffchange-inline">*[[</ins>Noncrystallographic symmetry<ins class="diffchange diffchange-inline">]]</ins>.  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; 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>D. M. Blow. ''International Tables for Crystallography'' (2006). Vol. F, ch. 13.1, pp. 263-268  [http://dx.doi.org/10.1107/97809553602060000681 doi:10.1107/97809553602060000681]  </div></td><td class='diff-marker'>+</td><td style="color:black; 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 class="diffchange diffchange-inline">*</ins>D. M. Blow. ''International Tables for Crystallography'' (2006). Vol. F, ch. 13.1, pp. 263-268  [http://dx.doi.org/10.1107/97809553602060000681 doi:10.1107/97809553602060000681]  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Biological crystallography]]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Biological crystallography]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Structure determination]]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Structure determination]]</div></td></tr>
</table>
MassimoNespolo
https://dictionary.iucr.org/index.php?title=Molecular_replacement&diff=2754&oldid=prev
BrianMcMahon at 10:53, 9 April 2008
2008-04-09T10:53:17Z
<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: white; color:black; text-align: center;">Revision as of 10:53, 9 April 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l11" >Line 11:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[Image:RTfunctioninMR.gif|frame|Figure 1. Illustration of the rotation and translation functions applied to superimpose a probe and target structure in molecular replacement.|right]]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[Image:RTfunctioninMR.gif|frame|Figure 1. Illustration of the rotation and translation functions applied to superimpose a probe and target structure in molecular replacement.|right]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; 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>Figure 1 illustrates schematically the process of repositioning the probe structure (the solid motif) in the new unit cell to coincide with the target structure (red outline motif). Rotation and transformation matrices must be applied. [[Patterson methods]] are suitable for determining the rotation function '''R''', since intramolecular vectors are all shifted to the origin of a Patterson map. The orientational fit (''i.e.'' the quality of the calculated rotation function) has usually been assessed by monitoring [[R factor|''R'' factors]] or [[real-space correlation coefficient]]s. Increasingly, modern programs use maximum likelihood based algorthms.  </div></td><td class='diff-marker'>+</td><td style="color:black; 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>Figure 1 illustrates schematically the process of repositioning the probe structure (the solid motif) in the new unit cell to coincide with the target structure (red outline motif). Rotation and transformation matrices must be applied. [[Patterson methods]] are suitable for determining the rotation function '''R''', since intramolecular vectors are all shifted to the origin of a Patterson map. The orientational fit (''i.e.'' the quality of the calculated rotation function) has usually been assessed by monitoring [[R factor|''R'' factors]] or [[real-space correlation coefficient]]s. Increasingly, modern programs use <ins class="diffchange diffchange-inline">[[</ins>maximum likelihood<ins class="diffchange diffchange-inline">]] </ins>based algorthms.  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The translation function '''T''' is then determined to shift the now correctly orientated probe model to the correct coordinates within the asymmetric unit. Space-group symmetries can be used to help reduce the computationally intense calculations required.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The translation function '''T''' is then determined to shift the now correctly orientated probe model to the correct coordinates within the asymmetric unit. Space-group symmetries can be used to help reduce the computationally intense calculations required.</div></td></tr>
</table>
BrianMcMahon
https://dictionary.iucr.org/index.php?title=Molecular_replacement&diff=2748&oldid=prev
AndreAuthier at 13:57, 8 April 2008
2008-04-08T13:57:06Z
<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr style="vertical-align: top;" lang="en">
<td colspan="2" style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: white; color:black; text-align: center;">Revision as of 13:57, 8 April 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; 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;"><Font color="blue"> Méthode du remplacement moléculaire </Font> (''Fr''). </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; 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: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Definition ==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Definition ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
</table>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Molecular_replacement&diff=2746&oldid=prev
BrianMcMahon at 11:21, 8 April 2008
2008-04-08T11:21:40Z
<p></p>
<p><b>New page</b></p><div>== Definition ==<br />
<br />
An approach to solving the [[phase problem]] by concentrating on phase relationships that arise through X-ray diffraction from similar molecular components. The components can be molecular fragments related through noncrystallographic symmetry (''e.g.'' icosahedral subunits of a virus) or a similar molecule such as a homologous protein with high sequence identity.<br />
<br />
== Discussion ==<br />
<br />
The technique is most commonly used in biological crystallography. Typically, an attempt is made to fit the structure under investigation (the 'target' structure) to a previously solved ('probe') structure. The probe may be a different crystal form of the same protein; or it may be a different protein with a high level of sequence identity, which correlates well with structural resemblance. As a rule of thumb, molecular replacement is often straightforward if the probe is well characterised and shares at least 40% sequence identity with the target.<br />
<br />
[[Image:RTfunctioninMR.gif|frame|Figure 1. Illustration of the rotation and translation functions applied to superimpose a probe and target structure in molecular replacement.|right]]<br />
<br />
Figure 1 illustrates schematically the process of repositioning the probe structure (the solid motif) in the new unit cell to coincide with the target structure (red outline motif). Rotation and transformation matrices must be applied. [[Patterson methods]] are suitable for determining the rotation function '''R''', since intramolecular vectors are all shifted to the origin of a Patterson map. The orientational fit (''i.e.'' the quality of the calculated rotation function) has usually been assessed by monitoring [[R factor|''R'' factors]] or [[real-space correlation coefficient]]s. Increasingly, modern programs use maximum likelihood based algorthms. <br />
<br />
The translation function '''T''' is then determined to shift the now correctly orientated probe model to the correct coordinates within the asymmetric unit. Space-group symmetries can be used to help reduce the computationally intense calculations required.<br />
<br />
== History ==<br />
<br />
Early applications of the technique concentrated on large virus structures with icosahedral symmetry. [Rossmann, M. G. &amp; Blow, D. M. (1962). [http://dx.doi.org/10.1107/S0365110X62000067 Acta Cryst. 15, 24–31]. ''The detection of sub-units within the crystallographic asymmetric unit.''] In the 1960s the early development of the molecular replacement technique was aimed primarily at ''ab initio'' phase determination. It was only in the 1970s, when more structures became available, that it was possible to use the technique to solve homologous structures with suitable search models.<br />
<br />
== See also ==<br />
<br />
Noncrystallographic symmetry.<br />
D. M. Blow. ''International Tables for Crystallography'' (2006). Vol. F, ch. 13.1, pp. 263-268 [http://dx.doi.org/10.1107/97809553602060000681 doi:10.1107/97809553602060000681] <br />
<br />
<br />
[[Category:Biological crystallography]]<br />
[[Category:Structure determination]]</div>
BrianMcMahon