https://proteopedia.org/index.php?action=history&feed=atom&title=User%3AWayne_Decatur%2F3ewsSLASH3g0h_Morph_methodsUser:Wayne Decatur/3ewsSLASH3g0h Morph methods - Revision history2026-09-24T08:02:34ZRevision history for this page on the wikiMediaWiki 1.43.8https://proteopedia.org/index.php?title=User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods&diff=1905250&oldid=prevWayne Decatur at 15:44, 20 March 20142014-03-20T15:44:45Z<p></p>
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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;"><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>'''I'd have to check but I think where I am using <code>structure TURN;</code> below, I probably wanted <code>structure NONE;</code>. The representation is the same except for color and so it worked for the purposes in which I used it here. But it wasn't probably the best way to do it.'''</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>'''I'd have to check but I think where I am using <code>structure TURN;</code> below, I probably wanted <code>structure NONE;</code>. The representation is the same except for color and so it worked for the purposes in which I used it here. But it wasn't probably the best way to do it.''' <ins style="font-weight: bold; text-decoration: none;">See [[Secondary structure]] and [http://wiki.jmol.org/index.php/Protein_Community here] and [http://chemapps.stolaf.edu/jmol/docs/?search=structure#structure here] and [http://chemapps.stolaf.edu/jmol/docs/?search=structure#setstructure here] for more information.</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;"><div>When the animation played in Jmol the models corresponding to 3ews and 3g0h had regions that should be turns that were showing as helices and beta sheets and so I used structure command to fix.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>When the animation played in Jmol the models corresponding to 3ews and 3g0h had regions that should be turns that were showing as helices and beta sheets and so I used structure command to fix.</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>select 67-90:a and 1.1;</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>select 67-90:a and 1.1;</div></td></tr>
</table>Wayne Decaturhttps://proteopedia.org/index.php?title=User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods&diff=1905249&oldid=prevWayne Decatur: /* Morph from 3ews to 3g0h structure */2014-03-20T15:40:46Z<p><span class="autocomment">Morph from 3ews to 3g0h structure</span></p>
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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;"><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 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;">'''I'd have to check but I think where I am using <code>structure TURN;</code> below, I probably wanted <code>structure NONE;</code>. The representation is the same except for color and so it worked for the purposes in which I used it here. But it wasn't probably the best way to do it.'''</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;"><div>When the animation played in Jmol the models corresponding to 3ews and 3g0h had regions that should be turns that were showing as helices and beta sheets and so I used structure command to fix.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>When the animation played in Jmol the models corresponding to 3ews and 3g0h had regions that should be turns that were showing as helices and beta sheets and so I used structure command to fix.</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>select 67-90:a and 1.1;</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>select 67-90:a and 1.1;</div></td></tr>
</table>Wayne Decaturhttps://proteopedia.org/index.php?title=User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods&diff=1102011&oldid=prevWayne Decatur at 23:59, 8 July 20102010-07-08T23:59:28Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:59, 8 July 2010</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>==Morph from 3ews to 3g0h structure==</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>==Morph from 3ews to 3g0h structure==</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><applet load='3g0h' size='300' frame='true' align='right' caption='Insert caption here' /></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><applet load='3g0h' size='300' frame='true' align='right' caption='Insert caption here' /></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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Ddx19morphback/1'><del style="font-weight: bold; text-decoration: none;">TextToBeDisplayed</del></scene></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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Ddx19morphback/1'><ins style="font-weight: bold; text-decoration: none;">Pre-hydrolysis (RNA and ATP bound) to post-hydrolysis (ADP bound)</ins></scene<ins style="font-weight: bold; text-decoration: none;">>.<br</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;"><div>Took the two files and submitted them. (Did it with 8 total models.)</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>Took the two files and submitted them. (Did it with 8 total models.)</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>The structures did have nucleic acids; however, I knew from past experience [http://molmovdb.org/cgi-bin/beta.cgi the beta server] handled them (even though it sitll says it will be updated to handle it) so I used it. (This time though the result just had chain A since I didn't have the nucleic in both 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>The structures did have nucleic acids; however, I knew from past experience [http://molmovdb.org/cgi-bin/beta.cgi the beta server] handled them (even though it sitll says it will be updated to handle it) so I used it. (This time though the result just had chain A since I didn't have the nucleic in both structures.)</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l12">Line 12:</td>
<td colspan="2" class="diff-lineno">Line 12:</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>Since the morph file that came back just had the protein from chain A from each endpoint structure, I added back the other parts (ligands and RNA, etc.) from 3ews to model 1 and the other parts of 3g0h to Model 8. </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>Since the morph file that came back just had the protein from chain A from each endpoint structure, I added back the other parts (ligands and RNA, etc.) from 3ews to model 1 and the other parts of 3g0h to Model 8. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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>However, while that worked for model 8, the ligand of model 1 was off to the side because it needed translating to where model 1 was in the morph which is not the same as 3ews. To move, I copied the 3ews part from the morph and opened it in Swiss-PDB Viewer. Then with MagicFit allowed in 'Loading protein' under preference, I loaded the actual 3ews pdb file. Then I saved the new layer and extracted the information for ADP and placed that as the ADP <del style="font-weight: bold; text-decoration: none;">heterotom </del>information in the Morph file for model 1. After doing that, I realized the first few residues of 3ews were missing too because they were absent in 3g0h and so I extracted the information fro them as well from the file and added them to the model 1 of the morph.</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>However, while that worked for model 8, the ligand of model 1 was off to the side because it needed translating to where model 1 was in the morph which is not the same as 3ews. To move, I copied the 3ews part from the morph and opened it in Swiss-PDB Viewer. Then with MagicFit allowed in 'Loading protein' under preference, I loaded the actual 3ews pdb file. Then I saved the new layer and extracted the information for ADP and placed that as the ADP <ins style="font-weight: bold; text-decoration: none;">heteratom </ins>information in the Morph file for model 1. After doing that, I realized the first few residues of 3ews were missing too because they were absent in 3g0h and so I extracted the information fro them as well from the file and added them to the model 1 of the morph.</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>Uploaded to Proteopedia [[Image:3ews3g0hmorphBETTER.pdb.gz]]. <br></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>Uploaded to Proteopedia [[Image:3ews3g0hmorphBETTER.pdb.gz]]. <br></div></td></tr>
</table>Wayne Decaturhttps://proteopedia.org/index.php?title=User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods&diff=1102010&oldid=prevWayne Decatur at 23:55, 8 July 20102010-07-08T23:55:10Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:55, 8 July 2010</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>==Morph from 3ews to 3g0h structure==</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>==Morph from 3ews to 3g0h structure==</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><applet load='3g0h' size='300' frame='true' align='right' caption='Insert caption here' /></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><applet load='3g0h' size='300' frame='true' align='right' caption='Insert caption here' /></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;"><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Ddx19morphback/1'>TextToBeDisplayed</scene></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;"><div>Took the two files and submitted them. (Did it with 8 total models.)</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>Took the two files and submitted them. (Did it with 8 total models.)</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>The structures did have nucleic acids; however, I knew from past experience [http://molmovdb.org/cgi-bin/beta.cgi the beta server] handled them (even though it sitll says it will be updated to handle it) so I used it. (This time though the result just had chain A since I didn't have the nucleic in both 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>The structures did have nucleic acids; however, I knew from past experience [http://molmovdb.org/cgi-bin/beta.cgi the beta server] handled them (even though it sitll says it will be updated to handle it) so I used it. (This time though the result just had chain A since I didn't have the nucleic in both structures.)</div></td></tr>
</table>Wayne Decaturhttps://proteopedia.org/index.php?title=User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods&diff=1046658&oldid=prevWayne Decatur at 20:55, 16 February 20102010-02-16T20:55:30Z<p></p>
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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;"><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>AS I SAW WITH 3fpn's file today: ENTERING 'model all;' INTO THE CONSOLE DOESNT WORK ON THESE FILES FROM YALE SERVER?!?! I assume it is the sever and not the number of models in the file because the 'model all' approach works with the ribosome files I made as well as LepA's files.</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>AS I SAW WITH 3fpn's file today: ENTERING 'model all;' INTO THE CONSOLE DOESNT WORK ON THESE FILES FROM YALE SERVER?!?! I assume it is the sever and not the number of models in the file because the 'model all' approach works with the ribosome files I made as well as LepA's files.</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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Testmodelall/1'>Test using console to enter model all command with the pdb file used in the morph</scene> uses ---->3ews3g0hmorphBETTER.pdb.gz at [[Image:3ews3g0hmorphBETTER.pdb.gz]].</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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Testmodelall/1'>Test using console to enter model all command with the pdb file used in the morph</scene> uses ---->3ews3g0hmorphBETTER.pdb.gz at [[Image:3ews3g0hmorphBETTER.pdb.gz]]. <ins style="font-weight: bold; text-decoration: none;">THE SCENE FAILS TO SHOW MORE THAN ONE MODEL!!!</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>Maybe it is the 'model 0' that Yale Moprh server puts because I was able to use 3ews3g0hJUSTSTARTEND.pdb which I simpled cut out in between models from first and last and made first model 1. Otherwise the formatting is like Yale Morph Server outputs.</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>Maybe it is the 'model 0' that Yale Moprh server puts because I was able to use 3ews3g0hJUSTSTARTEND.pdb which I simpled cut out in between models from first and last and made first model 1. Otherwise the formatting is like Yale Morph Server outputs.</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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Openclosedboth/10'>Testing where first model is 1 and not 0 like Yale Morph server puts</scene> uses ---->3ews3g0hJUSTSTARTEND.pdb.gz at [[Image:3ews3g0hJUSTSTARTEND.pdb.gz]].</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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Openclosedboth/10'>Testing where first model is 1 and not 0 like Yale Morph server puts</scene> uses ---->3ews3g0hJUSTSTARTEND.pdb.gz at [[Image:3ews3g0hJUSTSTARTEND.pdb.gz]].</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>YES IT MUST BE 'model 0' stuff or number of models because <scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Openclosedboth/10'><del style="font-weight: bold; text-decoration: none;">this</del></scene> <del style="font-weight: bold; text-decoration: none;">works</del>!!!!</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>YES IT MUST BE 'model 0' stuff or number of models because <scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Openclosedboth/10'><ins style="font-weight: bold; text-decoration: none;">THIS SCENE</ins></scene> <ins style="font-weight: bold; text-decoration: none;">WORKS</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>==Paper on the structure==</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>==Paper on the structure==</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><ref group="xtra">PMID:19244245</ref><references group="xtra"/></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><ref group="xtra">PMID:19244245</ref><references group="xtra"/></div></td></tr>
</table>Wayne Decaturhttps://proteopedia.org/index.php?title=User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods&diff=1046650&oldid=prevWayne Decatur at 20:48, 16 February 20102010-02-16T20:48:51Z<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 20:48, 16 February 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l132">Line 132:</td>
<td colspan="2" class="diff-lineno">Line 132:</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>AS I SAW WITH 3fpn's file today: ENTERING 'model all;' INTO THE CONSOLE DOESNT WORK ON THESE FILES FROM YALE SERVER?!?! I assume it is the sever and not the number of models in the file because the 'model all' approach works with the ribosome files I made as well as LepA's files.</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>AS I SAW WITH 3fpn's file today: ENTERING 'model all;' INTO THE CONSOLE DOESNT WORK ON THESE FILES FROM YALE SERVER?!?! I assume it is the sever and not the number of models in the file because the 'model all' approach works with the ribosome files I made as well as LepA's files.</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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Testmodelall/1'>Test using console to enter model all command with the pdb file used in the morph</scene> 3ews3g0hmorphBETTER.pdb.gz</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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Testmodelall/1'>Test using console to enter model all command with the pdb file used in the morph</scene<ins style="font-weight: bold; text-decoration: none;">> uses ----</ins>>3ews3g0hmorphBETTER.pdb.gz <ins style="font-weight: bold; text-decoration: none;">at [[Image:3ews3g0hmorphBETTER.pdb.gz]].</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>Maybe it is the 'model 0' that Yale Moprh server puts because I was able to use 3ews3g0hJUSTSTARTEND.pdb which I simpled cut out in between models from first and last and made first model 1. Otherwise the formatting is like Yale Morph Server outputs.</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>Maybe it is the 'model 0' that Yale Moprh server puts because I was able to use 3ews3g0hJUSTSTARTEND.pdb which I simpled cut out in between models from first and last and made first model 1. Otherwise the formatting is like Yale Morph Server outputs.</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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Openclosedboth/10'>Testing where first model is 1 and not 0 like Yale Morph server puts</scene></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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Openclosedboth/10'>Testing where first model is 1 and not 0 like Yale Morph server puts</scene> <ins style="font-weight: bold; text-decoration: none;">uses ---->3ews3g0hJUSTSTARTEND.pdb.gz at [[Image:3ews3g0hJUSTSTARTEND.pdb.gz]].</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;"><div>YES IT MUST BE 'model 0' stuff or number of models because <scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Openclosedboth/10'>this</scene> works!!!!</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>YES IT MUST BE 'model 0' stuff or number of models because <scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Openclosedboth/10'>this</scene> works!!!!</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>==Paper on the structure==</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>==Paper on the structure==</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><ref group="xtra">PMID:19244245</ref><references group="xtra"/></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><ref group="xtra">PMID:19244245</ref><references group="xtra"/></div></td></tr>
</table>Wayne Decaturhttps://proteopedia.org/index.php?title=User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods&diff=1046646&oldid=prevWayne Decatur at 20:07, 16 February 20102010-02-16T20:07:03Z<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 20:07, 16 February 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l134">Line 134:</td>
<td colspan="2" class="diff-lineno">Line 134:</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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Testmodelall/1'>Test using console to enter model all command with the pdb file used in the morph</scene> 3ews3g0hmorphBETTER.pdb.gz</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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Testmodelall/1'>Test using console to enter model all command with the pdb file used in the morph</scene> 3ews3g0hmorphBETTER.pdb.gz</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><del style="font-weight: bold; text-decoration: none;">Mayeb </del>it is the 'model 0' that Yale Moprh server puts because I was able to use 3ews3g0hJUSTSTARTEND.pdb which I simpled cut out in between models from first and last and made first model 1. Otherwise the formatting is like Yale Morph Server outputs.</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><ins style="font-weight: bold; text-decoration: none;">Maybe </ins>it is the 'model 0' that Yale Moprh server puts because I was able to use 3ews3g0hJUSTSTARTEND.pdb which I simpled cut out in between models from first and last and made first model 1. Otherwise the formatting is like Yale Morph Server outputs.</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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Openclosedboth/10'>Testing where first model is 1 and not 0 like Yale Morph server puts</scene></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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Openclosedboth/10'>Testing where first model is 1 and not 0 like Yale Morph server puts</scene></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;">YES IT MUST BE 'model 0' stuff or number of models because <scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Openclosedboth/10'>this</scene> works!!!!</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>==Paper on the structure==</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>==Paper on the structure==</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><ref group="xtra">PMID:19244245</ref><references group="xtra"/></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><ref group="xtra">PMID:19244245</ref><references group="xtra"/></div></td></tr>
</table>Wayne Decaturhttps://proteopedia.org/index.php?title=User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods&diff=1046645&oldid=prevWayne Decatur at 20:05, 16 February 20102010-02-16T20:05:40Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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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 20:05, 16 February 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l133">Line 133:</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>AS I SAW WITH 3fpn's file today: ENTERING 'model all;' INTO THE CONSOLE DOESNT WORK ON THESE FILES FROM YALE SERVER?!?! I assume it is the sever and not the number of models in the file because the 'model all' approach works with the ribosome files I made as well as LepA's files.</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>AS I SAW WITH 3fpn's file today: ENTERING 'model all;' INTO THE CONSOLE DOESNT WORK ON THESE FILES FROM YALE SERVER?!?! I assume it is the sever and not the number of models in the file because the 'model all' approach works with the ribosome files I made as well as LepA's files.</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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Testmodelall/1'>Test using console to enter model all command with the pdb file used in the morph</scene> 3ews3g0hmorphBETTER.pdb.gz</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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Testmodelall/1'>Test using console to enter model all command with the pdb file used in the morph</scene> 3ews3g0hmorphBETTER.pdb.gz</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;"></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;">Mayeb it is the 'model 0' that Yale Moprh server puts because I was able to use 3ews3g0hJUSTSTARTEND.pdb which I simpled cut out in between models from first and last and made first model 1. Otherwise the formatting is like Yale Morph Server outputs.</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;"><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Openclosedboth/10'>Testing where first model is 1 and not 0 like Yale Morph server puts</scene></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>==Paper on the structure==</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>==Paper on the structure==</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><ref group="xtra">PMID:19244245</ref><references group="xtra"/></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><ref group="xtra">PMID:19244245</ref><references group="xtra"/></div></td></tr>
</table>Wayne Decaturhttps://proteopedia.org/index.php?title=User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods&diff=1046644&oldid=prevWayne Decatur at 19:38, 16 February 20102010-02-16T19:38:26Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:38, 16 February 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l131">Line 131:</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>{{Template:Link Test template}}</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>{{Template:Link Test template}}</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 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;">AS I SAW WITH 3fpn's file today: ENTERING 'model all;' INTO THE CONSOLE DOESNT WORK ON THESE FILES FROM YALE SERVER?!?! I assume it is the sever and not the number of models in the file because the 'model all' approach works with the ribosome files I made as well as LepA's files.</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Testmodelall/1'>Test using console to enter model all command with the pdb file used in the morph</scene> 3ews3g0hmorphBETTER.pdb.gz</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><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Testmodelall/1'>Test using console to enter model all command with the pdb file used in the morph</scene> 3ews3g0hmorphBETTER.pdb.gz</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>==Paper on the structure==</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>==Paper on the structure==</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><ref group="xtra">PMID:19244245</ref><references group="xtra"/></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><ref group="xtra">PMID:19244245</ref><references group="xtra"/></div></td></tr>
</table>Wayne Decaturhttps://proteopedia.org/index.php?title=User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods&diff=1046641&oldid=prevWayne Decatur at 19:27, 16 February 20102010-02-16T19:27:45Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<col class="diff-marker" />
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<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 19:27, 16 February 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l130">Line 130:</td>
<td colspan="2" class="diff-lineno">Line 130:</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>The <scene name='3dmq/Rapa/1'>biological molecule is a single-chain RapA monomer</scene>.<br></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>The <scene name='3dmq/Rapa/1'>biological molecule is a single-chain RapA monomer</scene>.<br></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>{{Template:Link Test template}}</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>{{Template:Link Test template}}</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;"></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;"><scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Testmodelall/1'>Test using console to enter model all command with the pdb file used in the morph</scene> 3ews3g0hmorphBETTER.pdb.gz</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>==Paper on the structure==</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>==Paper on the structure==</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><ref group="xtra">PMID:19244245</ref><references group="xtra"/></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><ref group="xtra">PMID:19244245</ref><references group="xtra"/></div></td></tr>
</table>Wayne Decatur