https://wiki.pymol.org/index.php?action=history&feed=atom&title=Assembly 2026-04-30T10:30:05Z Revision history for this page on the wiki MediaWiki 1.35.1 https://wiki.pymol.org/index.php?title=Assembly&diff=13604&oldid=prev 2016-09-19T02:19:30Z

<p>1 revision</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 02:19, 19 September 2016</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=Assembly&diff=13603&oldid=prev 2016-09-01T13:27:01Z

<p>1.7.8 -&gt; 1.8</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 13:27, 1 September 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="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>When loading '''mmCIF''' structure files, the [[assembly]] setting controls whether PyMOL loads the asymmetric unit (assembly=&quot;&quot;) or a biological unit (e.g. assembly=&quot;1&quot;). Assembly identifiers in mmCIF files can be arbitrary strings, but usually are numeric and most files define at least assembly &quot;1&quot;.</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>When loading '''mmCIF''' structure files, the [[assembly]] setting controls whether PyMOL loads the asymmetric unit (assembly=&quot;&quot;) or a biological unit (e.g. assembly=&quot;1&quot;). Assembly identifiers in mmCIF files can be arbitrary strings, but usually are numeric and most files define at least assembly &quot;1&quot;.</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;"></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;"></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>''New in PyMOL 1<del class="diffchange diffchange-inline">.7</del>.8''</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>''New in PyMOL 1.8''</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;"></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;"></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>Assemblies with more than one symmetry copy are loaded as multi-state objects with [[all_states]]=on. The assemblies should be equivalent to the '''pdb1''' files which are available from the [ftp://ftp.wwpdb.org/pub/pdb/data/biounit/ PDB ftp server].</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>Assemblies with more than one symmetry copy are loaded as multi-state objects with [[all_states]]=on. The assemblies should be equivalent to the '''pdb1''' files which are available from the [ftp://ftp.wwpdb.org/pub/pdb/data/biounit/ PDB ftp server].</div></td></tr> </table>

Speleo3 https://wiki.pymol.org/index.php?title=Assembly&diff=12968&oldid=prev 2015-10-19T01:04:40Z

<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 01:04, 19 October 2015</td> </tr><tr><td colspan="2" class="diff-notice" lang="en"><div class="mw-diff-empty">(No difference)</div> </td></tr></table>

Bell https://wiki.pymol.org/index.php?title=Assembly&diff=12967&oldid=prev 2015-09-28T21:53:54Z

<p>BiologicalUnit/Quat link</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 21:53, 28 September 2015</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l24" >Line 24:</td> <td colspan="2" class="diff-lineno">Line 24:</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>* [[split_states]]</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>* [[split_states]]</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>* http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx.dic/Items/_pdbx_struct_assembly.id.html</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>* http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx.dic/Items/_pdbx_struct_assembly.id.html</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 style="font-weight: bold; text-decoration: none;">* [[BiologicalUnit/Quat]] and [[BiologicalUnit]]: scripts to parse assembly information from PDB files</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;"></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;"></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>[[Category:Settings]]</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>[[Category:Settings]]</div></td></tr> </table>

Speleo3 https://wiki.pymol.org/index.php?title=Assembly&diff=12966&oldid=prev 2015-09-28T21:50:59Z

<p>created</p> <p><b>New page</b></p><div>When loading '''mmCIF''' structure files, the [[assembly]] setting controls whether PyMOL loads the asymmetric unit (assembly=&quot;&quot;) or a biological unit (e.g. assembly=&quot;1&quot;). Assembly identifiers in mmCIF files can be arbitrary strings, but usually are numeric and most files define at least assembly &quot;1&quot;.<br /> <br /> ''New in PyMOL 1.7.8''<br /> <br /> Assemblies with more than one symmetry copy are loaded as multi-state objects with [[all_states]]=on. The assemblies should be equivalent to the '''pdb1''' files which are available from the [ftp://ftp.wwpdb.org/pub/pdb/data/biounit/ PDB ftp server].<br /> <br /> == Examples ==<br /> <br /> Download the ASU and the first assembly, show them side by side.<br /> <br /> &lt;syntaxhighlight lang=&quot;python&quot;&gt;<br /> set assembly, &quot;&quot;<br /> fetch 3bw1, asu, async=0<br /> <br /> set assembly, 1<br /> fetch 3bw1, assembly1, async=0<br /> <br /> set grid_mode<br /> &lt;/syntaxhighlight&gt;<br /> <br /> == See Also ==<br /> <br /> * [[all_states]]<br /> * [[split_states]]<br /> * http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx.dic/Items/_pdbx_struct_assembly.id.html<br /> <br /> [[Category:Settings]]</div>

Speleo3