https://pymolwiki.org/index.php?title=PyMOLProbity&feed=atom&action=history
PyMOLProbity - Revision history
2024-03-28T18:30:50Z
Revision history for this page on the wiki
MediaWiki 1.35.7
https://pymolwiki.org/index.php?title=PyMOLProbity&diff=12911&oldid=prev
Speleo3: conda
2019-04-25T10:40:44Z
<p>conda</p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 10:40, 25 April 2019</td>
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<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>For installation instructions, please see the [https://github.com/jaredsampson/pymolprobity/blob/master/README.md README] file in the </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>For installation instructions, please see the [https://github.com/jaredsampson/pymolprobity/blob/master/README.md README] file in the </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>[https://github.com/jaredsampson/pymolprobity repository].</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>[https://github.com/jaredsampson/pymolprobity repository].</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;"></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 style="font-weight: bold; text-decoration: none;">If you use [https://anaconda.org Anaconda], you can install the dependencies with:</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 style="font-weight: bold; text-decoration: none;"></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 style="font-weight: bold; text-decoration: none;"> conda install -c speleo3 reduce probe flipkin prekin</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>== Getting Started ==</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>== Getting Started ==</div></td></tr>
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Speleo3
https://pymolwiki.org/index.php?title=PyMOLProbity&diff=12505&oldid=prev
Jaredsampson: /* Description */ add link to repository
2017-01-16T04:19:26Z
<p><span dir="auto"><span class="autocomment">Description: </span> add link to repository</span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 04:19, 16 January 2017</td>
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<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>[[File:PyMOLProbity_GUI.png|480px|thumb|right|The PyMOLProbity GUI can be used to inspect and adjust clashes and flip orientations of flippable side chain groups.]]</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>[[File:PyMOLProbity_GUI.png|480px|thumb|right|The PyMOLProbity GUI can be used to inspect and adjust clashes and flip orientations of flippable side chain groups.]]</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>PyMOLProbity is a plugin allows the user to produce MolProbity-style</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">[https://github.com/jaredsampson/pymolprobity </ins>PyMOLProbity<ins class="diffchange diffchange-inline">] </ins>is a plugin allows the user to produce MolProbity-style</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>visualization of atomic interactions within a structure (e.g. H-bonds, van der</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>visualization of atomic interactions within a structure (e.g. H-bonds, van der</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>Waals interactions and clashes) directly within a PyMOL session. The plugin</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>Waals interactions and clashes) directly within a PyMOL session. The plugin</div></td></tr>
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Jaredsampson
https://pymolwiki.org/index.php?title=PyMOLProbity&diff=12504&oldid=prev
Jaredsampson: /* Getting Started */ Update GUI section.
2017-01-14T17:48:13Z
<p><span dir="auto"><span class="autocomment">Getting Started: </span> Update GUI section.</span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:48, 14 January 2017</td>
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<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>== Getting Started ==</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>== Getting Started ==</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>=== <del class="diffchange diffchange-inline">First run </del>===</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">GUI </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="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 class="diffchange diffchange-inline">Now you can open </del>PyMOL<del class="diffchange diffchange-inline">, load </del>or fetch a structure, and launch <del class="diffchange diffchange-inline">PyMOLProbity from</del></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">Once PyMOLProbity is installed, it should appear as an option in </ins>PyMOL<ins class="diffchange diffchange-inline">'s ''Plugin'' menu. Load </ins>or fetch a structure, and launch the <ins class="diffchange diffchange-inline">GUI by selecting ''</ins>Plugin <ins class="diffchange diffchange-inline">> PyMOLProbity''</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>the Plugin <del class="diffchange diffchange-inline">menu</del>. <del class="diffchange diffchange-inline"> </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;"></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>* Use the ''Add Hydrogens'' tab to add hydrogens with Reduce. This will also calculate which N/Q/H residue side chains should be flipped. </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>* Use the ''Add Hydrogens'' tab to add hydrogens with Reduce. This will also calculate which N/Q/H residue side chains should be flipped<ins class="diffchange diffchange-inline">, and perform those flips</ins>. <ins class="diffchange diffchange-inline">Note that this should be done even if the model already includes explicit hydrogens.</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>* <del class="diffchange diffchange-inline">If you would like to </del>examine these more closely, <del class="diffchange diffchange-inline">use </del>the ''Review Flips'' tab to <del class="diffchange diffchange-inline">examine </del>each flippable residue and choose the ones you wish to <del class="diffchange diffchange-inline">flip </del>or <del class="diffchange diffchange-inline">keep</del>.</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">To </ins>examine these more closely, <ins class="diffchange diffchange-inline">select </ins>the ''Review Flips'' tab<ins class="diffchange diffchange-inline">. Here, you can zoom </ins>to <ins class="diffchange diffchange-inline">inspect </ins>each flippable residue and choose the ones you wish to <ins class="diffchange diffchange-inline">keep </ins>or <ins class="diffchange diffchange-inline">change</ins>. <ins class="diffchange diffchange-inline"> </ins>Save <ins class="diffchange diffchange-inline">any changes </ins>using the <ins class="diffchange diffchange-inline">'''</ins>''Save Selections<ins class="diffchange diffchange-inline">'''</ins>'' button. </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><del class="diffchange diffchange-inline">* </del>Save <del class="diffchange diffchange-inline">these </del>using the ''Save Selections'' button. </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>* Finally, use the ''Visualize Contacts'' tab to run Probe on the modified coordinates and generate contact dots and clash vectors for all the atoms in your object.</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>* Finally, use the ''Visualize Contacts'' tab to run Probe on the modified coordinates and generate contact dots and clash vectors for all the atoms in your object.</div></td></tr>
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</table>
Jaredsampson
https://pymolwiki.org/index.php?title=PyMOLProbity&diff=12503&oldid=prev
Jaredsampson: Add screenshot.
2017-01-14T17:41:55Z
<p>Add screenshot.</p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:41, 14 January 2017</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l7" >Line 7:</td>
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<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>== Description ==</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>== Description ==</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>[[<del class="diffchange diffchange-inline">Image</del>:PyMOLProbity_GUI.png|480px|thumb|The PyMOLProbity GUI can be used to inspect and adjust clashes and flip orientations of flippable side chain groups.]]</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">File</ins>:PyMOLProbity_GUI.png|480px|thumb<ins class="diffchange diffchange-inline">|right</ins>|The PyMOLProbity GUI can be used to inspect and adjust clashes and flip orientations of flippable side chain groups.]]</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>PyMOLProbity is a plugin allows the user to produce MolProbity-style</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>PyMOLProbity is a plugin allows the user to produce MolProbity-style</div></td></tr>
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Jaredsampson
https://pymolwiki.org/index.php?title=PyMOLProbity&diff=12501&oldid=prev
Jaredsampson: Created page.
2017-01-14T05:52:15Z
<p>Created page.</p>
<p><b>New page</b></p><div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/jaredsampson/pymolprobity/raw/master/pymolprobity.tar.gz<br />
|author = [[User:jaredsampson|Jared Sampson]]<br />
|license = MIT<br />
}}<br />
<br />
== Description ==<br />
[[Image:PyMOLProbity_GUI.png|480px|thumb|The PyMOLProbity GUI can be used to inspect and adjust clashes and flip orientations of flippable side chain groups.]]<br />
<br />
PyMOLProbity is a plugin allows the user to produce MolProbity-style<br />
visualization of atomic interactions within a structure (e.g. H-bonds, van der<br />
Waals interactions and clashes) directly within a PyMOL session. The plugin<br />
runs local copies of several executable programs from the <br />
[http://kinemage.biochem.duke.edu/ Richardson Lab] at Duke University, <br />
authors of the [http://molprobity.biochem.duke.edu/ MolProbity] software, parses the output, and<br />
displays the results in the PyMOL viewport. There are both a graphical user<br />
interface (GUI) for general point-and-click use, and a command-line interface<br />
(CLI) suitable for scripting.<br />
<br />
== Installation ==<br />
<br />
For installation instructions, please see the [https://github.com/jaredsampson/pymolprobity/blob/master/README.md README] file in the <br />
[https://github.com/jaredsampson/pymolprobity repository].<br />
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== Getting Started ==<br />
<br />
=== First run ===<br />
<br />
Now you can open PyMOL, load or fetch a structure, and launch PyMOLProbity from<br />
the Plugin menu. <br />
<br />
* Use the ''Add Hydrogens'' tab to add hydrogens with Reduce. This will also calculate which N/Q/H residue side chains should be flipped. <br />
* If you would like to examine these more closely, use the ''Review Flips'' tab to examine each flippable residue and choose the ones you wish to flip or keep.<br />
* Save these using the ''Save Selections'' button. <br />
* Finally, use the ''Visualize Contacts'' tab to run Probe on the modified coordinates and generate contact dots and clash vectors for all the atoms in your object.<br />
<br />
=== Command-Line Interface ===<br />
<br />
The plugin makes the following functions available:<br />
<br />
* '''reduce_obj'''(obj, flip=1): Run reduce on a loaded PyMOL object (or named selection) with (default) or without making the Asn/Gln/His flips recommended by Reduce.<br />
<br />
* '''flipkin_obj'''(obj): Run Flipkin to create both NQ and H flipkin kinemage visualization of the Reduce-modified structure.<br />
<br />
* '''probe_obj'''(obj): Run Probe on either a structure saved from the Flipkin tab of the GUI, or the Reduce-modified structure.<br />
<br />
Note that both `flipkin_obj` and `probe_obj` require previously having run `reduce_obj` on the same object.<br />
<br />
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[[Category:Plugins]]</div>
Jaredsampson