https://wiki.pymol.org/index.php?action=history&feed=atom&title=Angle_between_domains 2026-06-13T17:34:14Z Revision history for this page on the wiki MediaWiki 1.35.1 https://wiki.pymol.org/index.php?title=Angle_between_domains&diff=13769&oldid=prev 2017-01-09T05:54:53Z

<p>2 revisions</p> <table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface"> <tr class="diff-title" lang="en"> <td colspan="1" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="1" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 05:54, 9 January 2017</td> </tr><tr><td colspan="2" class="diff-notice" lang="en"><div class="mw-diff-empty">(No difference)</div> </td></tr></table>

Cchem https://wiki.pymol.org/index.php?title=Angle_between_domains&diff=13768&oldid=prev 2016-12-21T15:01:01Z

<p>see also</p> <table class="diff diff-contentalign-left diff-editfont-monospace" 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 15:01, 21 December 2016</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 class='diff-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;">[[Category:Structural_Biology_Scripts]]</del></div></td><td colspan="2"> </td></tr> <tr><td class='diff-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 colspan="2"> </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>{{Infobox script-repo</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>{{Infobox script-repo</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>|type      = module</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>|type      = module</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l49" >Line 49:</td> <td colspan="2" class="diff-lineno">Line 47:</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>* [[AngleBetweenHelices]]</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>* [[AngleBetweenHelices]]</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>* [[align]], [[super]], [[cealign]]</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>* [[align]], [[super]], [[cealign]]</div></td></tr> <tr><td class='diff-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>* https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10995.html</div></td><td class='diff-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 class="diffchange diffchange-inline">[</ins>https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10995.html <ins class="diffchange diffchange-inline">pymol-users 01 Nov 2012]</ins></div></td></tr> <tr><td class='diff-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>* https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg13015.html</div></td><td class='diff-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 class="diffchange diffchange-inline">[</ins>https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg13015.html <ins class="diffchange diffchange-inline">pymol-users 13 Jan 2015]</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-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 class="diffchange diffchange-inline">* [[elbow_angle]]</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-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 class="diffchange diffchange-inline">* [[RotationAxis]]</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-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"> </td><td class='diff-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 class="diffchange diffchange-inline">[[Category:Structural_Biology_Scripts]]</ins></div></td></tr> </table>

Speleo3 https://wiki.pymol.org/index.php?title=Angle_between_domains&diff=13767&oldid=prev 2016-12-15T14:32:49Z

<p>created</p> <p><b>New page</b></p><div>[[Category:Structural_Biology_Scripts]]<br /> <br /> {{Infobox script-repo<br /> |type = module<br /> |download = [https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/orientation.py orientation.py]<br /> |author = [[User:Speleo3|Thomas Holder]]<br /> |license = BSD-2-Clause<br /> }}<br /> <br /> {{Infobox psico<br /> |module = psico.orientation<br /> }}<br /> <br /> '''angle_between_domains''' calculates the rotation and displacement that would happen when [[align|aligning]] two atom selections. The typical use case is for two conformations of a multi-domain structure, which is first aligned on domain 1 (e.g. chain A), and then '''angle_between_domains''' is calculated for domain 2 (e.g. chain B).<br /> <br /> == Usage ==<br /> <br /> angle_between_domains selection1, selection2 [, method<br /> [, state1 [, state2 [, visualize ]]]]<br /> <br /> == Arguments ==<br /> <br /> * '''selection1''' = str: atom selection in conformation 1<br /> * '''selection2''' = str: atom selection in conformation 2<br /> * '''method''' = str: alignment command like &quot;align&quot;, &quot;super&quot; or &quot;cealign&quot; {default: align}<br /> <br /> == Example ==<br /> <br /> &lt;syntaxhighlight lang=&quot;python&quot;&gt;<br /> # import the &quot;angle_between_domains&quot; command<br /> run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/orientation.py<br /> <br /> # two conformations of a two-chain structure<br /> fetch 1ake, s1, async=0<br /> fetch 4ake, s2, async=0<br /> <br /> # align on chain A<br /> align s1 &amp; chain A, s2 &amp; chain A<br /> <br /> # measure rotation and displacement of chain B<br /> angle_between_domains s1 &amp; chain B, s2 &amp; chain B<br /> &lt;/syntaxhighlight&gt;<br /> <br /> For 1ake and 4ake, this reports:<br /> Angle: 15.55 deg, Displacement: 56.08 angstrom<br /> <br /> == See also ==<br /> <br /> * [[AngleBetweenHelices]]<br /> * [[align]], [[super]], [[cealign]]<br /> * https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10995.html<br /> * https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg13015.html</div>

Speleo3