https://proteopedia.org/index.php?action=history&feed=atom&title=Jmol%2FVisualizing_large_molecules
Jmol/Visualizing large molecules - Revision history
2026-09-27T12:09:56Z
Revision history for this page on the wiki
MediaWiki 1.43.8
https://proteopedia.org/index.php?title=Jmol/Visualizing_large_molecules&diff=4211841&oldid=prev
Eric Martz at 13:46, 23 September 2024
2024-09-23T13:46:11Z
<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 13:46, 23 September 2024</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><Structure size='400' frame='true' align='right' caption='Half-capsid of human hepatitis B virus displaying only the alpha carbon atoms for the [[biological assembly]] of [[2g33]].' scene='Jmol/Visualizing_large_molecules/Backbone_by_chain/1' /></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><Structure size='400' frame='true' align='right' caption='Half-capsid of human hepatitis B virus displaying only the alpha carbon atoms for the [[biological assembly]] of [[2g33]].' scene='Jmol/Visualizing_large_molecules/Backbone_by_chain/1' /></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><center><table style="background-color:#d8ffd8;" class="wikitable"><tr><td></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><center><table style="background-color:#d8ffd8;" class="wikitable"><tr><td></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 page was written in 2011 and '''needs major revisions''' to take into account (i) that Proteopedia now automatically shows [[biological unit]] 1, simplified as needed (try [[4v60]] or [[1sva]]); (ii) the 2022 ability of [http://firstglance.jmol.org FirstGlance in Jmol] to automatically simplify and display very large [[biological units]];</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 page was written in 2011 and '''needs major revisions''' to take into account (i) that Proteopedia now automatically shows [[biological unit]] 1, simplified as needed (try [[4v60]] or [[1sva]]<ins style="font-weight: bold; text-decoration: none;"><ref>Page [[1sva]] uses the [[Molstar]] viewer instead of [[JSmol]].</ref></ins>); (ii) the 2022 ability of [http://firstglance.jmol.org FirstGlance in Jmol] to automatically simplify and display very large [[biological units]];</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>and (iii) the ability of JSmol to generate biological units. Please see:</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>and (iii) the ability of JSmol to generate biological units. Please see:</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>*[[Biological_Unit#Visualizing_the_Biological_Unit|Visualizing the Biological Unit]]</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>*[[Biological_Unit#Visualizing_the_Biological_Unit|Visualizing the Biological Unit]]</div></td></tr>
</table>
Eric Martz
https://proteopedia.org/index.php?title=Jmol/Visualizing_large_molecules&diff=4211839&oldid=prev
Eric Martz at 21:27, 22 September 2024
2024-09-22T21:27:03Z
<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 21:27, 22 September 2024</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l6">Line 6:</td>
<td colspan="2" class="diff-lineno">Line 6:</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>*[[FirstGlance/Virus_Capsids_and_Other_Large_Assemblies]]</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>*[[FirstGlance/Virus_Capsids_and_Other_Large_Assemblies]]</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>*[[Biological_Unit:_Showing]]</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>*[[Biological_Unit:_Showing]]</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>[[User:Eric Martz|Eric Martz]] <del style="font-weight: bold; text-decoration: none;">22</del>:<del style="font-weight: bold; text-decoration: none;">17</del>, <del style="font-weight: bold; text-decoration: none;">13 November 2022 </del>(UTC)</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>[[User:Eric Martz|Eric Martz]] <ins style="font-weight: bold; text-decoration: none;">21</ins>:<ins style="font-weight: bold; text-decoration: none;">27</ins>, <ins style="font-weight: bold; text-decoration: none;">22 September 2024 </ins>(UTC)</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></td></tr></table></center></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></td></tr></table></center></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>
</table>
Eric Martz
https://proteopedia.org/index.php?title=Jmol/Visualizing_large_molecules&diff=4211838&oldid=prev
Eric Martz at 21:26, 22 September 2024
2024-09-22T21:26:22Z
<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 21:26, 22 September 2024</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><Structure size='400' frame='true' align='right' caption='Half-capsid of human hepatitis B virus displaying only the alpha carbon atoms for the [[biological assembly]] of [[2g33]].' scene='Jmol/Visualizing_large_molecules/Backbone_by_chain/1' /></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><Structure size='400' frame='true' align='right' caption='Half-capsid of human hepatitis B virus displaying only the alpha carbon atoms for the [[biological assembly]] of [[2g33]].' scene='Jmol/Visualizing_large_molecules/Backbone_by_chain/1' /></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><center><table style="background-color:#d8ffd8;" class="wikitable"><tr><td></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><center><table style="background-color:#d8ffd8;" class="wikitable"><tr><td></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 page was written in 2011 and '''needs major revisions''' to take into account (i) that Proteopedia now automatically <del style="font-weight: bold; text-decoration: none;">simplifies large structures </del>(try [[4v60]] or [[1sva]]); (ii) the 2022 ability of [http://firstglance.jmol.org FirstGlance in Jmol] to automatically simplify and display very large [[biological units]];</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 page was written in 2011 and '''needs major revisions''' to take into account (i) that Proteopedia now automatically <ins style="font-weight: bold; text-decoration: none;">shows [[biological unit]] 1, simplified as needed </ins>(try [[4v60]] or [[1sva]]); (ii) the 2022 ability of [http://firstglance.jmol.org FirstGlance in Jmol] to automatically simplify and display very large [[biological units]];</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>and (iii) the ability of JSmol to generate biological units. Please see:</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>and (iii) the ability of JSmol to generate biological units. Please see:</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>*[[Biological_Unit#Visualizing_the_Biological_Unit|Visualizing the Biological Unit]]</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>*[[Biological_Unit#Visualizing_the_Biological_Unit|Visualizing the Biological Unit]]</div></td></tr>
</table>
Eric Martz
https://proteopedia.org/index.php?title=Jmol/Visualizing_large_molecules&diff=4211837&oldid=prev
Eric Martz at 21:22, 22 September 2024
2024-09-22T21:22:22Z
<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 21:22, 22 September 2024</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l2">Line 2:</td>
<td colspan="2" class="diff-lineno">Line 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><center><table style="background-color:#d8ffd8;" class="wikitable"><tr><td></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><center><table style="background-color:#d8ffd8;" class="wikitable"><tr><td></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>This page was written in 2011 and '''needs major revisions''' to take into account (i) that Proteopedia now automatically simplifies large structures (try [[4v60]] or [[1sva]]); (ii) the 2022 ability of [http://firstglance.jmol.org FirstGlance in Jmol] to automatically simplify and display very large [[biological units]];</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 page was written in 2011 and '''needs major revisions''' to take into account (i) that Proteopedia now automatically simplifies large structures (try [[4v60]] or [[1sva]]); (ii) the 2022 ability of [http://firstglance.jmol.org FirstGlance in Jmol] to automatically simplify and display very large [[biological units]];</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>and (<del style="font-weight: bold; text-decoration: none;">ii</del>) the ability of JSmol to generate biological units. Please see:</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>and (<ins style="font-weight: bold; text-decoration: none;">iii</ins>) the ability of JSmol to generate biological units. Please see:</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>*[[Biological_Unit#Visualizing_the_Biological_Unit|Visualizing the Biological Unit]]</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>*[[Biological_Unit#Visualizing_the_Biological_Unit|Visualizing the Biological Unit]]</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>*[[FirstGlance/Virus_Capsids_and_Other_Large_Assemblies]]</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>*[[FirstGlance/Virus_Capsids_and_Other_Large_Assemblies]]</div></td></tr>
</table>
Eric Martz
https://proteopedia.org/index.php?title=Jmol/Visualizing_large_molecules&diff=4211836&oldid=prev
Eric Martz at 21:20, 22 September 2024
2024-09-22T21:20:06Z
<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 21:20, 22 September 2024</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><Structure size='400' frame='true' align='right' caption='Half-capsid of human hepatitis B virus displaying only the alpha carbon atoms for the [[biological assembly]] of [[2g33]].' scene='Jmol/Visualizing_large_molecules/Backbone_by_chain/1' /></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><Structure size='400' frame='true' align='right' caption='Half-capsid of human hepatitis B virus displaying only the alpha carbon atoms for the [[biological assembly]] of [[2g33]].' scene='Jmol/Visualizing_large_molecules/Backbone_by_chain/1' /></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><center><table style="background-color:#d8ffd8;" class="wikitable"><tr><td></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><center><table style="background-color:#d8ffd8;" class="wikitable"><tr><td></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 page was written in 2011 and '''needs major revisions''' to take into account (i) the 2022 ability of [http://firstglance.jmol.org FirstGlance in Jmol] to automatically simplify and display very large [[biological units]];</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 page was written in 2011 and '''needs major revisions''' to take into account (i<ins style="font-weight: bold; text-decoration: none;">) that Proteopedia now automatically simplifies large structures (try [[4v60]] or [[1sva]]); (ii</ins>) the 2022 ability of [http://firstglance.jmol.org FirstGlance in Jmol] to automatically simplify and display very large [[biological units]];</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>and (ii) the ability of JSmol to generate biological units. Please see:</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>and (ii) the ability of JSmol to generate biological units. Please see:</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>*[[Biological_Unit#Visualizing_the_Biological_Unit|Visualizing the Biological Unit]]</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>*[[Biological_Unit#Visualizing_the_Biological_Unit|Visualizing the Biological Unit]]</div></td></tr>
</table>
Eric Martz
https://proteopedia.org/index.php?title=Jmol/Visualizing_large_molecules&diff=3663097&oldid=prev
Eric Martz at 22:17, 13 November 2022
2022-11-13T22:17:57Z
<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 22:17, 13 November 2022</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><Structure size='400' frame='true' align='right' caption='Half-capsid of human hepatitis B virus displaying only the alpha carbon atoms for the [[biological assembly]] of [[2g33]].' scene='Jmol/Visualizing_large_molecules/Backbone_by_chain/1' /></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><Structure size='400' frame='true' align='right' caption='Half-capsid of human hepatitis B virus displaying only the alpha carbon atoms for the [[biological assembly]] of [[2g33]].' scene='Jmol/Visualizing_large_molecules/Backbone_by_chain/1' /></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><center><table style="background-color:#<del style="font-weight: bold; text-decoration: none;">d80ffd8</del>;" class="wikitable"><tr><td></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><center><table style="background-color:#<ins style="font-weight: bold; text-decoration: none;">d8ffd8</ins>;" class="wikitable"><tr><td></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>This page was written in 2011 and '''needs major revisions''' to take into account (i) the 2022 ability of [http://firstglance.jmol.org FirstGlance in Jmol] to automatically simplify and display very large [[biological units]];</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 page was written in 2011 and '''needs major revisions''' to take into account (i) the 2022 ability of [http://firstglance.jmol.org FirstGlance in Jmol] to automatically simplify and display very large [[biological units]];</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>and (ii) the ability of JSmol to generate biological units. Please see:</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>and (ii) the ability of JSmol to generate biological units. Please see:</div></td></tr>
</table>
Eric Martz
https://proteopedia.org/index.php?title=Jmol/Visualizing_large_molecules&diff=3663096&oldid=prev
Eric Martz at 22:17, 13 November 2022
2022-11-13T22:17:09Z
<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 22:17, 13 November 2022</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><Structure size='400' frame='true' align='right' caption='Half-capsid of human hepatitis B virus displaying only the alpha carbon atoms for the [[biological assembly]] of [[2g33]].' scene='Jmol/Visualizing_large_molecules/Backbone_by_chain/1' /></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><Structure size='400' frame='true' align='right' caption='Half-capsid of human hepatitis B virus displaying only the alpha carbon atoms for the [[biological assembly]] of [[2g33]].' scene='Jmol/Visualizing_large_molecules/Backbone_by_chain/1' /></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;"><center><table style="background-color:#d80ffd8;" class="wikitable"><tr><td></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 page was written in 2011 and '''needs major revisions''' to take into account (i) the 2022 ability of [http://firstglance.jmol.org FirstGlance in Jmol] to automatically simplify and display very large [[biological units]];</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;">and (ii) the ability of JSmol to generate biological units. Please see:</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;">*[[Biological_Unit#Visualizing_the_Biological_Unit|Visualizing the Biological Unit]]</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;">*[[FirstGlance/Virus_Capsids_and_Other_Large_Assemblies]]</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;">*[[Biological_Unit:_Showing]]</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;">[[User:Eric Martz|Eric Martz]] 22:17, 13 November 2022 (UTC)</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;"></td></tr></table></center></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"></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>==Inadequate Memory May Preclude Display==</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>==Inadequate Memory May Preclude Display==</div></td></tr>
</table>
Eric Martz
https://proteopedia.org/index.php?title=Jmol/Visualizing_large_molecules&diff=3561177&oldid=prev
Eric Martz: /* 62 Chains */
2022-05-16T02:55:02Z
<p><span class="autocomment">62 Chains</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 02:55, 16 May 2022</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l30">Line 30:</td>
<td colspan="2" class="diff-lineno">Line 30:</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>In the final update of the PDB data format specification ([https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM Version 3.3]) and the current remediation of PDB data, chain IDs (names) must be single alphanumeric characters (A-Z, a-z, 0-9). This permits a maximum of 62 chains. This limit is not much of a problem for [[asymmetric unit|asymmetric units]]. In January, 2011, there is only one PDB entry with 62 chains ([[2zkr]]), and 4 more with 55-60 chains.</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>In the final update of the PDB data format specification ([https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM Version 3.3]) and the current remediation of PDB data, chain IDs (names) must be single alphanumeric characters (A-Z, a-z, 0-9). This permits a maximum of 62 chains. This limit is not much of a problem for [[asymmetric unit|asymmetric units]]. In January, 2011, there is only one PDB entry with 62 chains ([[2zkr]]), and 4 more with 55-60 chains.</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>Generally, the first 26 chains are given IDs A-Z. Above 26, it is apparently arbitrary whether numerals or lower case letters are used first. For example, for the 28 chains in [[3krd]] or [[3hln]] or [[3gpt]], those beyond A-Z are 1-2. Alternatively, for the 28 chains in [[3lo3]], the extra two are identified a-b, and in the 42-chain [[3jqo]], lower case ID's are present but no numerals. Also, when numerals are used, they may begin with 1, or with 0 ([[3fic]]). Occasionally, the letters A-Z are not used up before lower case ID's are employed: [[1tzn]] has 28 chains with ID's A-O and a-o.</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>Generally, the first 26 chains are given IDs A-Z. Above 26, it is apparently arbitrary whether numerals or lower case letters are used first. For example, for the 28 chains in [[3krd]] or [[3hln]] or [[3gpt]], those beyond A-Z are 1-2. Alternatively, for the 28 chains in [[3lo3]], the extra two are identified a-b, and in the 42-chain [[3jqo]], lower case ID's are present but no numerals. Also, when numerals are used, they may begin with 1, or with 0 ([[3fic]]). Occasionally, the letters A-Z are not used up before lower case ID's are employed: [[1tzn]] has 28 chains with ID's A-O and a-o<ins style="font-weight: bold; text-decoration: none;">. [[7sya]] has 12 chains a-l, with no chains having upper case names</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"></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>Jmol can automatically apply a distinct color to each chain, up to 36 chains ([http://jmol.sourceforge.net/jscolors/#Chains Jmol Colors]). However, it can distinguish 62 chains by selection (see [http://chemapps.stolaf.edu/jmol/docs/#setmisc set chainCaseSensitive]).</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>Jmol can automatically apply a distinct color to each chain, up to 36 chains ([http://jmol.sourceforge.net/jscolors/#Chains Jmol Colors]). However, it can distinguish 62 chains by selection (see [http://chemapps.stolaf.edu/jmol/docs/#setmisc set chainCaseSensitive]).</div></td></tr>
</table>
Eric Martz
https://proteopedia.org/index.php?title=Jmol/Visualizing_large_molecules&diff=3377674&oldid=prev
Eric Martz: /* 62 Chains */
2021-04-02T00:35:11Z
<p><span class="autocomment">62 Chains</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 00:35, 2 April 2021</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l28">Line 28:</td>
<td colspan="2" class="diff-lineno">Line 28:</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>===62 Chains===</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>===62 Chains===</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>In the final update of the PDB data format specification ([https://www.wwpdb.org/documentation/file-format-content/format33/<del style="font-weight: bold; text-decoration: none;">v3.3</del>.html#ATOM Version 3.3]) and the current remediation of PDB data, chain IDs (names) must be single alphanumeric characters (A-Z, a-z, 0-9). This permits a maximum of 62 chains. This limit is not much of a problem for [[asymmetric unit|asymmetric units]]. In January, 2011, there is only one PDB entry with 62 chains ([[2zkr]]), and 4 more with 55-60 chains.</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>In the final update of the PDB data format specification ([https://www.wwpdb.org/documentation/file-format-content/format33/<ins style="font-weight: bold; text-decoration: none;">sect9</ins>.html#ATOM Version 3.3]) and the current remediation of PDB data, chain IDs (names) must be single alphanumeric characters (A-Z, a-z, 0-9). This permits a maximum of 62 chains. This limit is not much of a problem for [[asymmetric unit|asymmetric units]]. In January, 2011, there is only one PDB entry with 62 chains ([[2zkr]]), and 4 more with 55-60 chains.</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>Generally, the first 26 chains are given IDs A-Z. Above 26, it is apparently arbitrary whether numerals or lower case letters are used first. For example, for the 28 chains in [[3krd]] or [[3hln]] or [[3gpt]], those beyond A-Z are 1-2. Alternatively, for the 28 chains in [[3lo3]], the extra two are identified a-b, and in the 42-chain [[3jqo]], lower case ID's are present but no numerals. Also, when numerals are used, they may begin with 1, or with 0 ([[3fic]]). Occasionally, the letters A-Z are not used up before lower case ID's are employed: [[1tzn]] has 28 chains with ID's A-O and a-o.</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>Generally, the first 26 chains are given IDs A-Z. Above 26, it is apparently arbitrary whether numerals or lower case letters are used first. For example, for the 28 chains in [[3krd]] or [[3hln]] or [[3gpt]], those beyond A-Z are 1-2. Alternatively, for the 28 chains in [[3lo3]], the extra two are identified a-b, and in the 42-chain [[3jqo]], lower case ID's are present but no numerals. Also, when numerals are used, they may begin with 1, or with 0 ([[3fic]]). Occasionally, the letters A-Z are not used up before lower case ID's are employed: [[1tzn]] has 28 chains with ID's A-O and a-o.</div></td></tr>
</table>
Eric Martz
https://proteopedia.org/index.php?title=Jmol/Visualizing_large_molecules&diff=3377673&oldid=prev
Eric Martz at 00:34, 2 April 2021
2021-04-02T00:34:24Z
<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 00:34, 2 April 2021</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l28">Line 28:</td>
<td colspan="2" class="diff-lineno">Line 28:</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>===62 Chains===</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>===62 Chains===</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>In the <del style="font-weight: bold; text-decoration: none;">most recent </del>update of the PDB data format specification ([<del style="font-weight: bold; text-decoration: none;">http</del>://www.wwpdb.org/documentation/<del style="font-weight: bold; text-decoration: none;">format32</del>/<del style="font-weight: bold; text-decoration: none;">sect9</del>.html#ATOM Version 3.<del style="font-weight: bold; text-decoration: none;">2, October 2008</del>]), chain IDs (names) must be single alphanumeric characters (A-Z, a-z, 0-9). This permits a maximum of 62 chains. This limit is not much of a problem for [[asymmetric unit|asymmetric units]]. In January, 2011, there is only one PDB entry with 62 chains ([[2zkr]]), and 4 more with 55-60 chains.</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>In the <ins style="font-weight: bold; text-decoration: none;">final </ins>update of the PDB data format specification ([<ins style="font-weight: bold; text-decoration: none;">https</ins>://www.wwpdb.org/documentation/<ins style="font-weight: bold; text-decoration: none;">file-format-content</ins>/<ins style="font-weight: bold; text-decoration: none;">format33/v3.3</ins>.html#ATOM Version 3.<ins style="font-weight: bold; text-decoration: none;">3</ins>]) <ins style="font-weight: bold; text-decoration: none;">and the current remediation of PDB data</ins>, chain IDs (names) must be single alphanumeric characters (A-Z, a-z, 0-9). This permits a maximum of 62 chains. This limit is not much of a problem for [[asymmetric unit|asymmetric units]]. In January, 2011, there is only one PDB entry with 62 chains ([[2zkr]]), and 4 more with 55-60 chains.</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>Generally, the first 26 chains are given IDs A-Z. Above 26, it is apparently arbitrary whether numerals or lower case letters are used first. For example, for the 28 chains in [[3krd]] or [[3hln]] or [[3gpt]], those beyond A-Z are 1-2. Alternatively, for the 28 chains in [[3lo3]], the extra two are identified a-b, and in the 42-chain [[3jqo]], lower case ID's are present but no numerals. Also, when numerals are used, they may begin with 1, or with 0 ([[3fic]]). Occasionally, the letters A-Z are not used up before lower case ID's are employed: [[1tzn]] has 28 chains with ID's A-O and a-o.</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>Generally, the first 26 chains are given IDs A-Z. Above 26, it is apparently arbitrary whether numerals or lower case letters are used first. For example, for the 28 chains in [[3krd]] or [[3hln]] or [[3gpt]], those beyond A-Z are 1-2. Alternatively, for the 28 chains in [[3lo3]], the extra two are identified a-b, and in the 42-chain [[3jqo]], lower case ID's are present but no numerals. Also, when numerals are used, they may begin with 1, or with 0 ([[3fic]]). Occasionally, the letters A-Z are not used up before lower case ID's are employed: [[1tzn]] has 28 chains with ID's A-O and a-o.</div></td></tr>
</table>
Eric Martz