https://pymolwiki.org/index.php?title=Category:Modeling_and_Editing_Structures&feed=atom&action=history
Category:Modeling and Editing Structures - Revision history
2024-03-29T13:27:46Z
Revision history for this page on the wiki
MediaWiki 1.35.7
https://pymolwiki.org/index.php?title=Category:Modeling_and_Editing_Structures&diff=3224&oldid=prev
Krother at 13:42, 14 December 2006
2006-12-14T13:42:35Z
<p></p>
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<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 13:42, 14 December 2006</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l214" >Line 214:</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> editor.attach_fragment('pk1','my_fragment_name',11,0)</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> editor.attach_fragment('pk1','my_fragment_name',11,0)</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>where my_fragment_name is the name of the pkl-file (w/o .pkl extension) and 11 is the number of the connecting (hydrogen) atom in the fragment. <del class="diffchange diffchange-inline">(I don't know exactly how to </del>determine this number, <del class="diffchange diffchange-inline">except trial </del>and <del class="diffchange diffchange-inline">error)</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>where my_fragment_name is the name of the pkl-file (w/o .pkl extension) and 11 is the number of the connecting (hydrogen) atom in the fragment. </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">To </ins>determine this number, <ins class="diffchange diffchange-inline">press '[L]abel' -> 'atom identifiers' -> 'index' </ins>and <ins class="diffchange diffchange-inline">choose the hydrogen atom you want</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>If you want a hotkey for your fragment, you can probably put it in <pymol_path>/modules/pmg_tk/skins/normal/__init__.py, but I haven't tried this.</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>If you want a hotkey for your fragment, you can probably put it in <pymol_path>/modules/pmg_tk/skins/normal/__init__.py, but I haven't tried this.</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:Advanced Issues|Modeling and Editing Structures]]</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:Advanced Issues|Modeling and Editing Structures]]</div></td></tr>
</table>
Krother
https://pymolwiki.org/index.php?title=Category:Modeling_and_Editing_Structures&diff=1775&oldid=prev
Epf: /* Modeling in PyMOL */
2006-01-10T16:03:27Z
<p><span dir="auto"><span class="autocomment">Modeling in PyMOL</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:03, 10 January 2006</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l201" >Line 201:</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>Protect one object, deprotect the other, grab the deprotected object and move with Shift-Mouse. </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>Protect one object, deprotect the other, grab the deprotected object and move with Shift-Mouse. </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>Don't forget to switch to Mouse Editing mode.</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>Don't forget to switch to Mouse Editing mode.</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;"></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;">==Adding and using your own fragments==</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;">Pymol has some build-in fragments (amino acids and simple functional groups). You can add your own fragments, eg. sugars, in this way:</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;">Create the molecule you want to use as a fragment. Save it as a .pkl file in <pymol_path>/data/chempy/fragments.</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;">How to use the fragment:</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;">Pick the atom (ctrl-middle) where you want to add the fragment. This will usually be a hydrogen atom (which will be removed). Then use the command:</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;"> editor.attach_fragment('pk1','my_fragment_name',11,0)</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;">where my_fragment_name is the name of the pkl-file (w/o .pkl extension) and 11 is the number of the connecting (hydrogen) atom in the fragment. (I don't know exactly how to determine this number, except trial and error).</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;">If you want a hotkey for your fragment, you can probably put it in <pymol_path>/modules/pmg_tk/skins/normal/__init__.py, but I haven't tried this.</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:Advanced Issues|Modeling and Editing Structures]]</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:Advanced Issues|Modeling and Editing Structures]]</div></td></tr>
</table>
Epf
https://pymolwiki.org/index.php?title=Category:Modeling_and_Editing_Structures&diff=1276&oldid=prev
Vladimircho: /* Manual superposition of two molecules */
2005-10-01T02:24:45Z
<p><span dir="auto"><span class="autocomment">Manual superposition of two molecules</span></span></p>
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<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 02:24, 1 October 2005</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l199" >Line 199:</td>
<td colspan="2" class="diff-lineno">Line 199:</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>You can also align to structures using mouse rotation/translation. For this, you need to protect those molecules you don't want to move with (action menu -> movement -> protect) in the selection menu.</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>You can also align to structures using mouse rotation/translation. For this, you need to protect those molecules you don't want to move with (action menu -> movement -> protect) in the selection menu.</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>Protect one <del class="diffchange diffchange-inline">molecule</del>, deprotect the other, and move with Shift-Mouse. Don't forget to switch to Mouse Editing mode.</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>Protect one <ins class="diffchange diffchange-inline">object</ins>, deprotect the other, <ins class="diffchange diffchange-inline">grab the deprotected object </ins>and move with Shift-Mouse. </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>Don't forget to switch to Mouse Editing mode.</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:Advanced Issues|Modeling and Editing Structures]]</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:Advanced Issues|Modeling and Editing Structures]]</div></td></tr>
</table>
Vladimircho
https://pymolwiki.org/index.php?title=Category:Modeling_and_Editing_Structures&diff=1102&oldid=prev
Vladimircho: /* Manual superposition of two molecules */
2005-10-01T02:08:00Z
<p><span dir="auto"><span class="autocomment">Manual superposition of two molecules</span></span></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
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<col class="diff-marker" />
<col class="diff-content" />
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<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 02:08, 1 October 2005</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l198" >Line 198:</td>
<td colspan="2" class="diff-lineno">Line 198:</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>==Manual superposition of two molecules==</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>==Manual superposition of two molecules==</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>You can also align to structures using mouse rotation/translation. For this, you need to protect those molecules you don't want to move with (action menu -> movement -> protect) in the selection menu.</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>You can also align to structures using mouse rotation/translation. For this, you need to protect those molecules you don't want to move with (action menu -> movement -> protect) in the selection menu.</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;">Protect one molecule, deprotect the other, and move with Shift-Mouse. Don't forget to switch to Mouse Editing mode.</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:Advanced Issues|Modeling and Editing Structures]]</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:Advanced Issues|Modeling and Editing Structures]]</div></td></tr>
</table>
Vladimircho
https://pymolwiki.org/index.php?title=Category:Modeling_and_Editing_Structures&diff=1101&oldid=prev
Inchoate at 20:55, 6 May 2005
2005-05-06T20:55:29Z
<p></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 20:55, 6 May 2005</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l199" >Line 199:</td>
<td colspan="2" class="diff-lineno">Line 199:</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>You can also align to structures using mouse rotation/translation. For this, you need to protect those molecules you don't want to move with (action menu -> movement -> protect) in the selection menu.</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>You can also align to structures using mouse rotation/translation. For this, you need to protect those molecules you don't want to move with (action menu -> movement -> protect) in the selection menu.</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>[[Category:<del class="diffchange diffchange-inline">Modeling_and_Editing_Structures</del>|Modeling and Editing Structures]]</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>[[Category:<ins class="diffchange diffchange-inline">Advanced Issues</ins>|Modeling and Editing Structures]]</div></td></tr>
</table>
Inchoate
https://pymolwiki.org/index.php?title=Category:Modeling_and_Editing_Structures&diff=684&oldid=prev
Inchoate at 20:54, 6 May 2005
2005-05-06T20:54:30Z
<p></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 20:54, 6 May 2005</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l199" >Line 199:</td>
<td colspan="2" class="diff-lineno">Line 199:</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>You can also align to structures using mouse rotation/translation. For this, you need to protect those molecules you don't want to move with (action menu -> movement -> protect) in the selection menu.</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>You can also align to structures using mouse rotation/translation. For this, you need to protect those molecules you don't want to move with (action menu -> movement -> protect) in the selection menu.</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>[[Category:<del class="diffchange diffchange-inline">Advanced_Issues</del>|Modeling and Editing Structures]]</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>[[Category:<ins class="diffchange diffchange-inline">Modeling_and_Editing_Structures</ins>|Modeling and Editing Structures]]</div></td></tr>
</table>
Inchoate
https://pymolwiki.org/index.php?title=Category:Modeling_and_Editing_Structures&diff=683&oldid=prev
Inchoate at 20:51, 6 May 2005
2005-05-06T20:51:37Z
<p></p>
<p><b>New page</b></p><div>=Modeling in PyMOL=<br />
<br />
==Saving with transformed coordinates==<br />
<br />
Here is a simple script that saves the molecule with coordinates from the current orientation.<br />
(invoke it with 'run save_transformed.py' and type the new save_transformed.py command thereafter).<br />
<source lang="python"><br />
# Adds the command save_transformed<br />
# Usage: save_transformed object, file<br />
def save_transformed(object,file):<br />
m = cmd.get_view(0)<br />
ttt = [m[0], m[1], m[2], 0.0,<br />
m[3], m[4], m[5], 0.0,<br />
m[6], m[7], m[8], 0.0,<br />
0.0, 0.0, 0.0, 1.0]<br />
cmd.transform_object(object,ttt)<br />
cmd.save(file,object)<br />
<br />
cmd.extend('save_transformed',save_transformed)<br />
</source><br />
<br />
<br />
==Translate or rotate individual objects==<br />
There is a "translate" function similar to "rotate", the docs for these don't exist yet, because the implementation isn't finished. However, feel free to use them in the following forms:<br />
<br />
<source lang="python"><br />
translate vector,object-name,state<br />
(vector needs to be something like [x,y,z])<br />
<br />
translate [1,0,0],pept<br />
<br />
rotate axis,angle,object-name,state<br />
(axis can be either the letter x,y,z or a 3D vector [x,y,z])<br />
rotate x,90,pept<br />
rotate [1,1,1],10,pept<br />
</source><br />
<br />
==Moving one segment relative to the rest==<br />
<br />
This means moving two parts of one object into different directions. The easiest way to do this is to split the objects and then use the rotate command.<br />
<source lang="python"><br />
load 1FJ1.pdb<br />
<br />
# split PDB file<br />
<br />
create anti=(chain F) <br />
create fab=(chain A,B)<br />
<br />
# delete original object<br />
delete 1FJ1<br />
<br />
# color objects<br />
color green,fab<br />
color pink,anti<br />
<br />
# color interface<br />
select inter = (byres ((fab within 5 of anti)\<br />
or (anti within 5 of fab)))<br />
<br />
color yellow,inter<br />
<br />
# splay apart<br />
orient<br />
origin fab<br />
rotate y,60,fab<br />
origin anti<br />
rotate y,-60, anti<br />
<br />
# zoom interface region<br />
zoom inter<br />
show sph,inter<br />
disable inter<br />
</source><br />
<br />
==Split states to objects==<br />
There is also a new command in the 0.95 series:<br />
<source lang="python"><br />
split_states object-name<br />
</source><br />
which will spread a PDB "biological unit" (or any multi-state object -- including SD files) over a series of independent objects. This makes it possible to interact with such objects more naturally than with "all_states = 1".<br />
<br />
<br />
<br />
==Altering secondary structures==<br />
<br />
Examples:<br />
<source lang="python"><br />
alter A/10:34/, ss='H'<br />
alter A/35:40/, ss='L'<br />
alter A/41:60/, ss='S'<br />
</source><br />
<br />
==Altering van der Waals radii==<br />
<br />
Example:<br />
<source lang="python"><br />
alter (elem Fe),vdw=1.8<br />
rebuild<br />
</source><br />
(The value for Fe is wrecked in PyMOL at the moment, so running the above line might be a good idea).<br />
<br />
<br />
==Altering atom coordinates==<br />
<br />
Example:<br />
<source lang="python"><br />
alter_state 1,(pdb1cse),x=x-10.0 <br />
</source><br />
The latter section can contain formulae involving at least the xyz coordinates, lots of constants and the (+-*/) operators.<br />
<br />
<br />
==Deleting bonds==<br />
<br />
Select the bond using Ctrl-right-click, then either<br />
<source lang="python"><br />
unbond pk1,pk2<br />
</source><br />
or hit Ctrl-D.<br />
<br />
<br />
==Converting D- to L- amino acids==<br />
The inversion function was changed in version 0.95 to take advantage of multiple picked atoms. To invert a center, Ctrl-middle-click to pick the center atom as pk1 and two stationary atoms as pk2 and pk3. Then type Ctrl-E to invert.<br />
<br />
<br />
==Adding disulfide bonds==<br />
You can use the [[Cmd bond]] command to attach them:<br />
<source lang="python"><br />
bond 24/sg,26/sg<br />
bond 56/sg,99/sg<br />
unpick<br />
</source><br />
(unpick will hide the bond baton which gets displayed.)<br />
Additionally, the residue names can be changed for bonded cysteines:<br />
<source lang="python"><br />
alter cys/,name='CYX'<br />
</source><br />
or for specific residues<br />
<source lang="python"><br />
alter 24+26+56+99/,name='CYX'<br />
</source><br />
<br />
<br />
==Adding hydrogen bonds==<br />
See 'displaying biochemical properties'.<br />
<br />
<br />
==Protonating ligands==<br />
If your ligands come in with valid valencies and formal charges, PyMOL's h_add command can protonate ligands. (NOTE that there is a minor technical hiccup with SD-files which are loaded by default as immutable "discrete" objects.) Suffice it to say that in order to make changes to the chemical structure, an object must be loaded with the "discrete" flag set to zero.<br />
Unfortunately, much of the molecular editing stuff remains to be documented. Here's an example sequence, but I'm not sure it will help to much...as indicated in the manual, this is immature functionality with some major gaps. Attach in particular is very limited...<br />
<br />
<source lang="python"><br />
# show valences<br />
set valence=0.05<br />
<br />
# load cysteine fragment<br />
fragment cys<br />
<br />
# remove hydrogens<br />
remove (hydro)<br />
<br />
# edit gamma S<br />
edit cys////sg<br />
<br />
# add hydrogen<br />
attach H,1,1<br />
<br />
# add planer, trivalent nitrogen onto C terminus<br />
edit cys////C<br />
attach N,3,3<br />
<br />
# edit that nitrogen<br />
edit (elem N and neighbor cys////C)<br />
<br />
# attach a tetrahedral methyl (note random position)<br />
attach C,4,4<br />
<br />
# here's an example of adding a whole residue from the library<br />
edit cys////N<br />
editor.attach_amino_acid("pk1","ace")<br />
<br />
# now restore missing hydrogens (note that the names are off...)<br />
h_add<br />
</source><br />
<br />
<br />
==Superposition of two molecules==<br />
Using pair_fit requires that you specify a set of paired atoms in each structure. Fortunately, you no longer have to specify each pair separately, so long as the ordering is the same in each selection (almost always true).<br />
<source lang="python"><br />
pair_fit ( trna10 and resid 10:15 and name P ), ( ref4 and resid 10:15 and name P )<br />
</source><br />
<br />
Another example:<br />
<source lang="python"><br />
pair_fit prot1///11-26/CA, prot2///34-49/CA<br />
</source><br />
would superimpose prot1 on prot2 using C-alphas from residues 11-26 in prot1 and 34-49 in prot2.<br />
<br />
==Manual superposition of two molecules==<br />
You can also align to structures using mouse rotation/translation. For this, you need to protect those molecules you don't want to move with (action menu -> movement -> protect) in the selection menu.<br />
<br />
[[Category:Advanced_Issues|Modeling and Editing Structures]]</div>
Inchoate