http://52.214.119.220/wiki/index.php?action=history&feed=atom&title=User%3AShai_Biran%2FPractice_Proteopedia_tutorial_shai5 2026-04-12T09:31:38Z Revision history for this page on the wiki MediaWiki 1.11.2 http://52.214.119.220/wiki/index.php?title=User:Shai_Biran/Practice_Proteopedia_tutorial_shai5&diff=2407492&oldid=prev 2015-06-01T12:51:35Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 12:51, 1 June 2015</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 26:</td> <td colspan="2" class="diff-lineno">Line 26:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Now that we have everything selected, click on the “representations” tab of the SAT.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Now that we have everything selected, click on the “representations” tab of the SAT.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Representations.png]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Representations.png]]</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Mark the checkbox next to “backbone” in the section titled “set selection representation”.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Mark the checkbox next to “backbone” in the section titled “set selection representation”.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Click on the “set representation” button. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Click on the “set representation” button. </div></td></tr> </table>

Shai Biran http://52.214.119.220/wiki/index.php?title=User:Shai_Biran/Practice_Proteopedia_tutorial_shai5&diff=2407488&oldid=prev 2015-06-01T12:34:07Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 12:34, 1 June 2015</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 45:</td> <td colspan="2" class="diff-lineno">Line 45:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[User:Shai Biran/Practice Proteopedia tutorial <del style="color: red; font-weight: bold; text-decoration: none;">shai5</del>|Previous page (<del style="color: red; font-weight: bold; text-decoration: none;">6</del>)]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[User:Shai Biran/Practice Proteopedia tutorial <ins style="color: red; font-weight: bold; text-decoration: none;">shai4</ins>|Previous page (<ins style="color: red; font-weight: bold; text-decoration: none;">5</ins>)]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[User:Shai Biran/Practice Proteopedia tutorial <del style="color: red; font-weight: bold; text-decoration: none;">shai7</del>|Next Page (<del style="color: red; font-weight: bold; text-decoration: none;">8</del>)]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[User:Shai Biran/Practice Proteopedia tutorial <ins style="color: red; font-weight: bold; text-decoration: none;">shai6</ins>|Next Page (<ins style="color: red; font-weight: bold; text-decoration: none;">7</ins>)]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

Shai Biran http://52.214.119.220/wiki/index.php?title=User:Shai_Biran/Practice_Proteopedia_tutorial_shai5&diff=2379393&oldid=prev 2015-02-25T15:54:23Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 15:54, 25 February 2015</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 39:</td> <td colspan="2" class="diff-lineno">Line 39:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Hover_over_atom.png]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Hover_over_atom.png]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Enter the starting and ending residue numbers, separated by a <del style="color: red; font-weight: bold; text-decoration: none;">hypen</del>, into the input box under the text “limit to residue numbers:”.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Enter the starting and ending residue numbers, separated by a <ins style="color: red; font-weight: bold; text-decoration: none;">hyphen</ins>, into the input box under the text “limit to residue numbers:”<ins style="color: red; font-weight: bold; text-decoration: none;">.</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Before making our new selection, let’s turn on selection halos so we see the change in the selection take place. Mark the checkbox next to “selection halos”. Notice that everything is selected.</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Now go ahead and make the new selection by clicking “replace selection”. This will replace the old selection (everything) with our new selection (limited to a stretch of residues)</ins>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Next ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Next ==</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

Shai Biran http://52.214.119.220/wiki/index.php?title=User:Shai_Biran/Practice_Proteopedia_tutorial_shai5&diff=2379388&oldid=prev 2015-02-25T15:39:30Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 15:39, 25 February 2015</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 38:</td> <td colspan="2" class="diff-lineno">Line 38:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Hover_over_atom.png]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Hover_over_atom.png]]</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Enter the starting and ending residue numbers, separated by a hypen, into the input box under the text “limit to residue numbers:”.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Enter the starting and ending residue numbers, separated by a hypen, into the input box under the text “limit to residue numbers:”.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Next ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Next ==</div></td></tr> </table>

Shai Biran http://52.214.119.220/wiki/index.php?title=User:Shai_Biran/Practice_Proteopedia_tutorial_shai5&diff=2379387&oldid=prev 2015-02-25T15:39:09Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 15:39, 25 February 2015</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 36:</td> <td colspan="2" class="diff-lineno">Line 36:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We will select the segment that runs through the barrel by its residue numbers. To do this we need to know the first and the last residue numbers that make up this segment.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We will select the segment that runs through the barrel by its residue numbers. To do this we need to know the first and the last residue numbers that make up this segment.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Notice that when you hover with your mouse over an atom in the Jmol applet, information about that atom is displayed, including the residue that atom is part of, and the residue number. Use this “hover” feature to find the residue numbers for the beginning and the end of the segment we are interested in.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Notice that when you hover with your mouse over an atom in the Jmol applet, information about that atom is displayed, including the residue that atom is part of, and the residue number. Use this “hover” feature to find the residue numbers for the beginning and the end of the segment we are interested in.</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:Hover_over_atom.png]]</div></td><td colspan="2">&nbsp;</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Hover_over_atom.png]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Enter the starting and ending residue numbers, separated by a hypen, into the input box under the text “limit to residue numbers:”.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Enter the starting and ending residue numbers, separated by a hypen, into the input box under the text “limit to residue numbers:”.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Next ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Next ==</div></td></tr> </table>

Shai Biran http://52.214.119.220/wiki/index.php?title=User:Shai_Biran/Practice_Proteopedia_tutorial_shai5&diff=2379386&oldid=prev 2015-02-25T15:38:38Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 15:38, 25 February 2015</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 31:</td> <td colspan="2" class="diff-lineno">Line 31:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Backbones.png]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Backbones.png]]</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Now we want to select the segment of the protein that runs through the barrel and color it green.</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>To make a selection, click on the “selections” tab.</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We will select the segment that runs through the barrel by its residue numbers. To do this we need to know the first and the last residue numbers that make up this segment.</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Notice that when you hover with your mouse over an atom in the Jmol applet, information about that atom is displayed, including the residue that atom is part of, and the residue number. Use this “hover” feature to find the residue numbers for the beginning and the end of the segment we are interested in.</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Hover_over_atom.png]]</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Enter the starting and ending residue numbers, separated by a hypen, into the input box under the text “limit to residue numbers:”.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Next ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Next ==</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

Shai Biran http://52.214.119.220/wiki/index.php?title=User:Shai_Biran/Practice_Proteopedia_tutorial_shai5&diff=2379378&oldid=prev 2015-02-25T15:11:57Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 15:11, 25 February 2015</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 29:</td> <td colspan="2" class="diff-lineno">Line 29:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Click on the “set representation” button. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Click on the “set representation” button. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Notice the representation of the 3D model has changed from cartoon to backbone. To help see this better, turn off the selection halos by unmarking the checkbox next to “selection halos”.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Notice the representation of the 3D model has changed from cartoon to backbone. To help see this better, turn off the selection halos by unmarking the checkbox next to “selection halos”.</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Backbones.png]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Backbones.png]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Next ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Next ==</div></td></tr> </table>

Shai Biran http://52.214.119.220/wiki/index.php?title=User:Shai_Biran/Practice_Proteopedia_tutorial_shai5&diff=2379377&oldid=prev 2015-02-25T15:08:53Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 15:08, 25 February 2015</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 24:</td> <td colspan="2" class="diff-lineno">Line 24:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Selection halos serve to show you what is currently selected. They will not be displayed when the green scene link you eventually create is clicked.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Selection halos serve to show you what is currently selected. They will not be displayed when the green scene link you eventually create is clicked.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Now that we have everything selected, click on the “representations” tab of the SAT.</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Representations.png]]</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Mark the checkbox next to “backbone” in the section titled “set selection representation”.</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Click on the “set representation” button. </div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Notice the representation of the 3D model has changed from cartoon to backbone. To help see this better, turn off the selection halos by unmarking the checkbox next to “selection halos”.</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Backbones.png]]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Next ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Next ==</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

Shai Biran http://52.214.119.220/wiki/index.php?title=User:Shai_Biran/Practice_Proteopedia_tutorial_shai5&diff=2379374&oldid=prev 2015-02-25T14:54:09Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 14:54, 25 February 2015</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 7:</td> <td colspan="2" class="diff-lineno">Line 7:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>use the 'show preview' button to check what changed in your page.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>use the 'show preview' button to check what changed in your page.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>----</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>----</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Now that we have our 3D model on the page, let’s create a green scene link that shows 1ema as it looks in the the left part of the 2D image on the GFP Sample page where we got our text. (go back to that page to see what the picture looks like<del style="color: red; font-weight: bold; text-decoration: none;">) </del>[[User:Shai Biran/GFP test page]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Now that we have our 3D model on the page, let’s create a green scene link that shows 1ema as it looks in the the left part of the 2D image on the GFP Sample page where we got our text. (go back to that page to see what the picture looks like [[User:Shai Biran/GFP test page]]<ins style="color: red; font-weight: bold; text-decoration: none;">)</ins></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>To create a green scene link, we will need to use the '<del style="color: red; font-weight: bold; text-decoration: none;">Protopedia </del>Scene Authoring Tools'. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>To create a green scene link, we will need to use the '<ins style="color: red; font-weight: bold; text-decoration: none;">Proteopedia </ins>Scene Authoring Tools'. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*After clicking '''edit this page''', scroll down to the bold text that says “Scene authoring tools [show]” next to a colorful molecule. Click on “show” to expand the Scene Authoring Tools.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*After clicking '''edit this page''', scroll down to the bold text that says “Scene authoring tools [show]” next to a colorful molecule. Click on “show” to expand the Scene Authoring Tools.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:SAT.png]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:SAT.png]]</div></td></tr> </table>

Shai Biran http://52.214.119.220/wiki/index.php?title=User:Shai_Biran/Practice_Proteopedia_tutorial_shai5&diff=2379373&oldid=prev 2015-02-25T14:50:54Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 14:50, 25 February 2015</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 15:</td> <td colspan="2" class="diff-lineno">Line 15:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Now we have 1ema loaded into the Scene Authoring Tools’ Jmol applet. The idea behind the Scene Authoring Tools (SAT) is to create the exact scene that you would like to have load when your green link is clicked. This is generally done by first loading a PDB file into the SAT’s applet, then using the “selections”, “representations”, “colors”, and “labels” tabs to manipulate the 3D model into the desired state, finally saving the green scene link using the “save scene” tab.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Now we have 1ema loaded into the Scene Authoring Tools’ Jmol applet. The idea behind the Scene Authoring Tools (SAT) is to create the exact scene that you would like to have load when your green link is clicked. This is generally done by first loading a PDB file into the SAT’s applet, then using the “selections”, “representations”, “colors”, and “labels” tabs to manipulate the 3D model into the desired state, finally saving the green scene link using the “save scene” tab.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Our structure is currently displayed in cartoon representation. The first step in recreating the picture in the Molecule of the Month is to display the molecule in backbone representation.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Our structure is currently displayed in cartoon representation. The first step in recreating the picture in the Molecule of the Month is to display the molecule in backbone representation.</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">*</del>*Click on the “selections” tab.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*Click on the “selections” tab.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Selections.png]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Selections.png]]</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">*</del>*In the “all or nothing and halos” section, click on the “select all” button.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*In the “all or nothing and halos” section, click on the “select all” button.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:GFP_Halos_off.png]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:GFP_Halos_off.png]]</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">*</del>*Nothing changed because “selection halos” were not on. Turn them on by marking the checkbox next to the word “selection halos”. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*Nothing changed because “selection halos” were not on. Turn them on by marking the checkbox next to the word “selection halos”. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:GFP_Halos_On.png]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:GFP_Halos_On.png]]</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Selection halos serve to show you what is currently selected. They will not be displayed when the green scene link you eventually create is clicked.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Selection halos serve to show you what is currently selected. They will not be displayed when the green scene link you eventually create is clicked.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

Shai Biran