https://script.spoken-tutorial.org/index.php?action=history&feed=atom&title=Jmol-Application%2FC2%2FStructures-from-Database%2FEnglish 2026-05-14T11:13:03Z Revision history for this page on the wiki MediaWiki 1.23.17 https://script.spoken-tutorial.org/index.php?title=Jmol-Application/C2/Structures-from-Database/English&diff=48897&oldid=prev 2019-08-26T12:30:57Z

<p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td> <td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 12:30, 26 August 2019</td> </tr><tr><td colspan="2" class="diff-lineno">Line 332:</td> <td colspan="2" class="diff-lineno">Line 332:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>| style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Here is another assignment for you.</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>| style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Here is another assignment for you.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">&#160; </del>1. Draw 2D structures of the following '''Amino acids''' in '''GChemPaint.'''</div></td><td class='diff-marker'>+</td><td style="color:black; 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>1. Draw 2D structures of the following '''Amino acids''' in '''GChemPaint.'''</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">&#160; </del>* '''Cysteine '''</div></td><td class='diff-marker'>+</td><td style="color:black; 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>* '''Cysteine '''</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">&#160; </del>* '''Histidine '''</div></td><td class='diff-marker'>+</td><td style="color:black; 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>* '''Histidine '''</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">&#160; </del>* '''Phenylalanine'''</div></td><td class='diff-marker'>+</td><td style="color:black; 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>* '''Phenylalanine'''</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">&#160; </del>2. Save as '''.mol '''files.</div></td><td class='diff-marker'>+</td><td style="color:black; 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>2. Save as '''.mol '''files.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>&#160;&#160; &#160;</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>&#160;&#160; &#160;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">&#160; </del>3. Open the files in '''Jmol''' and modify the display. &#160;</div></td><td class='diff-marker'>+</td><td style="color:black; 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>3. Open the files in '''Jmol''' and modify the display. &#160;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td></tr> </table>

Snehalathak https://script.spoken-tutorial.org/index.php?title=Jmol-Application/C2/Structures-from-Database/English&diff=48896&oldid=prev 2019-08-26T12:29:33Z

<p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td> <td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 12:29, 26 August 2019</td> </tr><tr><td colspan="2" class="diff-lineno">Line 332:</td> <td colspan="2" class="diff-lineno">Line 332:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>| style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Here is another assignment for you.</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>| style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Here is another assignment for you.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">&#160; </del>1. Draw 2D structures of the following '''Amino acids''' in '''GChemPaint.'''</div></td><td class='diff-marker'>+</td><td style="color:black; 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">&#160; </ins>1. Draw 2D structures of the following '''Amino acids''' in '''GChemPaint.'''</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline"> </del>* '''Cysteine '''</div></td><td class='diff-marker'>+</td><td style="color:black; 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">&#160; </ins>* '''Cysteine '''</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline"> </del>* '''Histidine '''</div></td><td class='diff-marker'>+</td><td style="color:black; 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">&#160; </ins>* '''Histidine '''</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline"> </del>* '''Phenylalanine'''</div></td><td class='diff-marker'>+</td><td style="color:black; 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">&#160; </ins>* '''Phenylalanine'''</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">&#160; </del>2. Save as '''.mol '''files.</div></td><td class='diff-marker'>+</td><td style="color:black; 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">&#160; </ins>2. Save as '''.mol '''files.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>&#160;&#160; &#160;</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>&#160;&#160; &#160;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">&#160; </del>3. Open the files in '''Jmol''' and modify the display. &#160;</div></td><td class='diff-marker'>+</td><td style="color:black; 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">&#160; </ins>3. Open the files in '''Jmol''' and modify the display. &#160;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td></tr> </table>

Snehalathak https://script.spoken-tutorial.org/index.php?title=Jmol-Application/C2/Structures-from-Database/English&diff=48895&oldid=prev 2019-08-26T12:28:33Z

<p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td> <td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 12:28, 26 August 2019</td> </tr><tr><td colspan="2" class="diff-lineno">Line 332:</td> <td colspan="2" class="diff-lineno">Line 332:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>| style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Here is another assignment for you.</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>| style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Here is another assignment for you.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline"> </del>1. Draw 2D structures of the following '''Amino acids''' in '''GChemPaint.'''</div></td><td class='diff-marker'>+</td><td style="color:black; 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">&#160; </ins>1. Draw 2D structures of the following '''Amino acids''' in '''GChemPaint.'''</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; 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>* '''Cysteine '''</div></td><td class='diff-marker'>+</td><td style="color:black; 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"> </ins>* '''Cysteine '''</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; 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>* '''Histidine '''</div></td><td class='diff-marker'>+</td><td style="color:black; 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"> </ins>* '''Histidine '''</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; 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>* '''Phenylalanine'''</div></td><td class='diff-marker'>+</td><td style="color:black; 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"> </ins>* '''Phenylalanine'''</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline"> </del>2. Save as '''.mol '''files.</div></td><td class='diff-marker'>+</td><td style="color:black; 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">&#160; </ins>2. Save as '''.mol '''files.</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline"> </del>3. Open the files in '''Jmol''' and modify the display. &#160;</div></td><td class='diff-marker'>+</td><td style="color:black; 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">&#160; </ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; 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">&#160; </ins>3. Open the files in '''Jmol''' and modify the display. &#160;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td></tr> </table>

Snehalathak https://script.spoken-tutorial.org/index.php?title=Jmol-Application/C2/Structures-from-Database/English&diff=48894&oldid=prev 2019-08-26T12:27:33Z

<p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td> <td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 12:27, 26 August 2019</td> </tr><tr><td colspan="2" class="diff-lineno">Line 332:</td> <td colspan="2" class="diff-lineno">Line 332:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>| style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Here is another assignment for you.</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>| style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Here is another assignment for you.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline"># </del>Draw structures of the following '''Amino acids''' in '''GChemPaint.'''</div></td><td class='diff-marker'>+</td><td style="color:black; 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"> 1. </ins>Draw <ins class="diffchange diffchange-inline">2D </ins>structures of the following '''Amino acids''' in '''GChemPaint.'''</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* '''Cysteine '''</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* '''Cysteine '''</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 338:</td> <td colspan="2" class="diff-lineno">Line 338:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* '''Phenylalanine'''</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* '''Phenylalanine'''</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline"># </del>Save <del class="diffchange diffchange-inline">the 2D structures </del>as '''.mol '''files.</div></td><td class='diff-marker'>+</td><td style="color:black; 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"> 2. </ins>Save as '''.mol '''files.</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline"># </del>Open <del class="diffchange diffchange-inline">these </del>files in '''Jmol''' and modify the display. &#160;</div></td><td class='diff-marker'>+</td><td style="color:black; 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"> 3. </ins>Open <ins class="diffchange diffchange-inline">the </ins>files in '''Jmol''' and modify the display. &#160;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td></tr> </table>

Snehalathak https://script.spoken-tutorial.org/index.php?title=Jmol-Application/C2/Structures-from-Database/English&diff=9791&oldid=prev 2014-04-09T05:11:47Z

<p>Created page with &#039;&#039;&#039;&#039;Title of script&#039;&#039;&#039;: Structures from Database &#039;&#039;&#039;Author: Snehalatha Kaliappan&#039;&#039;&#039; &#039;&#039;&#039;Keywords: Video tutorial, Chemical structures from Database, Jmol video tutorial&#039;&#039;&#039; {| st…&#039;</p> <p><b>New page</b></p><div>'''Title of script''': Structures from Database<br /> <br /> '''Author: Snehalatha Kaliappan'''<br /> <br /> '''Keywords: Video tutorial, Chemical structures from Database, Jmol video tutorial'''<br /> <br /> {| style=&quot;border-spacing:0;&quot;<br /> ! &lt;center&gt;Visual Cue&lt;/center&gt;<br /> ! &lt;center&gt;Narration&lt;/center&gt;<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| '''Slide Number 1'''<br /> <br /> '''Title Slide'''<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Welcome to this tutorial on '''Structures from Databases in Jmol'''<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| '''Slide Number 2'''<br /> <br /> '''Learning Objectives'''<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| In this tutorial, we will learn to<br /> <br /> * Load chemical structures from '''PubChem''' database.&lt;br/&gt; And<br /> * Convert 2D structures drawn in '''GChemPaint''' to 3D models in '''Jmol'''.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| '''Slide Number 3'''<br /> <br /> '''Pre-requisites'''<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| To follow this tutorial you should be familiar with '''Jmol Application'''.<br /> <br /> If not, watch the relevant tutorials available at our website. <br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| '''Slide Number 4'''<br /> <br /> '''System Requirement'''<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| To record this tutorial I am using <br /> <br /> <br /> * '''Ubuntu Linux '''OS version. 12.04<br /> * '''Jmol''' version 12.2.2<br /> * '''Java''' version 7<br /> * '''GChemPaint''' version 0.12.10<br /> * '''Mozilla Firefox''' browser 22.0<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on the panel<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| I have opened a new '''Jmol Application''' window.<br /> <br /> <br /> '''Jmol''' has a feature to load structures of compounds listed in the database.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Click on the 'File' menu.<br /> <br /> Scroll down the menu.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| The ''''File'''' menu on the menu bar, has an option ''''Get MOL'.'''<br /> <br /> This loads molecules from chemical structure data base ''''PubChem'.'''<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on 'Get PDB'.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| It also has another option ''''Get PDB'''' to load protein structures from '''Protein Data Bank'''. <br /> <br /> This feature will be explained in detail in another tutorial.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Click on 'Get Mol'.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| To load a chemical structure on the panel, click on ''''Get Mol''''.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on the 'Input' dialog box.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| An ''''Input'''' dialog box opens on the screen.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| '''Slide Number 5'''<br /> <br /> '''Identification of Molecules'''<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Any molecule listed in the database can be loaded by typing the following in the text box:<br /> <br /> * Common name or '''IUPAC''' name <br /> * '''CAS '''number ('''Chemical Abstracts Service''') registry number<br /> * '''CID''' number (Compound Identification Number). <br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| '''Slide Number 6'''<br /> <br /> '''Identification of Molecules'''<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| * InChi identifier (IUPAC International Chemical Identifier or<br /> * SMILES identifier that is ('''S'''implified '''M'''olecular '''I'''nput '''L'''ine '''E'''ntry '''S'''ystem)<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Switch to the browser with the Pubchem database website.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Please visit '''Pubchem''' database website for information on identification numbers for a particular chemical<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Type '''Phenol''' in the text box.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| let us display '''phenol''' on screen.<br /> <br /> <br /> So type ''''phenol'''' in the '''Input '''text box.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Press OK button.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Press '''OK''' button.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on '''Phenol'''.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Model of '''phenol''' is displayed on panel.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on the panel.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| We can modify the display of '''phenol''' using various rendering options.<br /> <br /> These options are listed in '''Menu bar '''and '''Pop'''-'''up menu'''. <br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Click on '''display''' menu, and select''' label'''. Click on '''number''' from the options. <br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| We can add substituents to the '''benzene''' '''ring''' of '''phenol'''.<br /> <br /> First let us label the atoms in the model.<br /> <br /> Click on '''display''' menu, and select''' label'''. Click on '''number '''option. <br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on the panel.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Now, let's replace a '''hydrogen number 10 '''attached to '''carbon atom number 4 '''with an amino group'''.'''<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Open '''modelkit menu''', select '''nitrogen'''. <br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Open the '''modelkit menu''' select '''nitrogen from options'''. <br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Click on '''hydrogen''' attached to '''Atom number 3.'''<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Click on '''hydrogen number 10'''.<br /> <br /> This is a molecule of '''Para-Amino Phenol''' on the '''panel'''.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Open pop-up menu, scroll to '''style and '''select '''sticks''' from the options.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| We will change the display to '''Sticks display'''.<br /> <br /> Exit the modelkit menu.<br /> <br /> Open the Pop-up menu, scroll down to '''Style '''and''' '''select '''Scheme.''' Select '''Sticks''' from the options.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on the panel.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| On the panel we have a model of Para-Amino-phenol in sticks display.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Type '''cholesterol''' in the text box'''. '''<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Complex structures, which are difficult to create, can easily be loaded on the '''panel'''.<br /> <br /> For example '''cholesterol.''' <br /> <br /> Click on file menu<br /> <br /> '''Click on Get Mol''' option once again and type '''Cholesterol '''in the text box.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Press OK button.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Press '''OK''' button.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on the panel.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| A molecule of '''Cholesterol '''is displayed''' '''on the '''panel'''. <br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on the double-bond and side-chain.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| We can highlight the features like '''double-bond''' and '''side-chain '''in the molecule'''.'''<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on the panel.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| To highlight double-bond, first let us change the color of '''carbon''' atoms of the double-bond. <br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Click on ''''Select a set of atoms'''' icon in the tool bar.<br /> <br /> Click on Carbons involved in double-bond<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Click on ''''Select atoms'''' icon in the tool bar.<br /> <br /> Then click on the '''carbon''' atoms involved in the double-bond.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on the yellow halo. <br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| A yellow halo appears around the atoms.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Right click on the panel, scroll down to ''''Colors'''', select ''''Atoms'''' then click on '''Orange'''. <br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Open the Pop-up-menu.<br /> <br /> Scroll down to '''Color''', select '''Atoms''' and click on '''Orange''' option. <br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Click anywhere on the '''panel'''.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Click on “Rotate molecule” option in the tool bar.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on the double-bond.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| The double-bond in the '''cholesterol '''model is now in orange color.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Click on ''''Select a set of atoms'''' icon in the tool bar.<br /> <br /> Click on all the atoms of the side-chain.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Similarly, we can highlight the '''carbons '''in the side-chain.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Right click on the panel, scroll down to ''''Colors'''', select ''''Atoms'''' then click on '''Violet'''. <br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Using '''Pop-up'''-menu change the color to violet.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on the panel.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| On the '''panel, '''we have a model of '''Cholesterol '''with important features highlighted. <br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| '''Slide Number 7'''<br /> <br /> '''Assignment'''<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| As an assignment,<br /> <br /> * Load structure of caffeine from '''Pubchem''' database .<br /> * Highlight the important features in the molecule.<br /> * Modify the display to '''wireframe'''.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on panel with Alanine.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Now I will discuss another important feature of '''Jmol.'''<br /> <br /> We can convert 2D structures of molecules drawn in another software into 3D models.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on panel with Alanine.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Here I have a model of '''aminoacid Alanine''' on the panel.<br /> <br /> 2D structure of this molecule was drawn in software called '''GChemPaint.'''<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on panel with Alanine.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| The structure was saved as''' a .mol '''file. <br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| '''Slide Number 8'''<br /> <br /> '''About GChemPaint'''<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| '''GchemPaint '''is an Open source software for drawing 2D chemical structures.<br /> <br /> Tutorials on '''GChemPaint '''are available at the following link.<br /> <br /> To draw structures and save in .mol format, refer to Analysis of Compounds tutorial.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Open GchemPaint window load 2D -structures of Alanine, <br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Shown on this Gchempaint display area are 2D drawings of <br /> <br /> * '''Amino acid -Alanine'''<br /> * '''Nuclioside -Adenosine'''<br /> * '''Saccharide -Alpha-D glucopyranose'''<br /> <br /> I have saved them in '''.mol '''format on my '''Desktop.'''<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on the panel.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| First, let's view the 2D structure of '''Alanine '''as 3D model in '''Jmol Application'''.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Exit the GchemPaint program.<br /> <br /> Open a new Jmol window.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| So, I will open a new '''Jmol '''window.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Click on 'Open a file 'option in the tool bar.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Click on ''''Open a file'''' icon in the tool bar.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Click on Desktop and click open button.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| I will choose '''Desktop''' folder and click on open. Choose the file '''Alanine.mol '''and click on '''Open''' button.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on the screen.<br /> <br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| A 3D model of ''''Alanine'''' opens on screen.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Click on modelkit icon and scroll down the menu and click on 'fix hydrogens and minimize' option.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Open the '''modelkit menu '''and click on ''''fix hydrogens and minimize'''' option.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on the panel.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| '''Hydrogens''' are added to the structure and the energy minimized.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Cursor on menu bar.<br /> <br /> Right click on the panel to open the Pop-up menu.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| As with any '''.mol''' file, we can change the display using menu bar and also '''Pop-up '''menu. <br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Open the model of '''Adenosine''' on screen.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Here is the 3D model of '''Adenosine.mol '''in '''Jmol.'''<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| Open the model of '''Alpha D glucopyranose '''on jmol panel.<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| And this is a 3D model of '''Alpha-D-glucopyranose.mol '''in '''Jmol.'''<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| '''Slide Number 9'''<br /> <br /> '''Summary'''<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Let's summarize <br /> <br /> In this tutorial we have learnt to<br /> <br /> <br /> * Load chemical structures from '''Pubchem''' data base. <br /> * Modify the display of '''Phenol''' and '''Cholesterol'''. &lt;br/&gt; <br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| '''Slide Number 10'''<br /> <br /> '''Summary'''<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| * Convert 2D structures drawn in '''GChemPaint''' to 3D models in '''Jmol'''.<br /> * Convert 2D structures of '''Alanine, Adenosine''' and '''Alpha-D-glucopyranose '''to 3D models.<br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| '''Slide Number 11'''<br /> <br /> '''Assignment'''<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Here is another assignment for you.<br /> <br /> # Draw structures of the following '''Amino acids''' in '''GChemPaint.'''<br /> <br /> * '''Cysteine '''<br /> * '''Histidine '''<br /> * '''Phenylalanine'''<br /> <br /> # Save the 2D structures as '''.mol '''files.<br /> # Open these files in '''Jmol''' and modify the display. <br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| '''Slide Number 12'''<br /> <br /> '''Acknowledgement '''<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Watch the video available at this URL.<br /> <br /> h[http://spoken-tutorial.org/What ttp://spoken-tutorial.org/What]_is_a_Spoken_ Tutorial<br /> <br /> It summarizes the Spoken Tutorial project<br /> <br /> If you do not have good bandwidth, you can download and watch it <br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| '''Slide Number 13'''<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| The Spoken Tutorial Project Team: <br /> <br /> Conducts workshops using spoken tutorials<br /> <br /> Gives certificates to those who pass an on-line test <br /> <br /> For more details, please write to <br /> <br /> contact@spoken-tutorial.org <br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| '''Slide number 14'''<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| Spoken Tutorial Project is a part of the Talk to a Teacher project <br /> <br /> It is supported by the National Mission on Education through ICT, MHRD, Government of India<br /> <br /> More information on this Mission is available at this link [http://spoken-tutorial.org/NMEICT-Intro http://spoken-tutorial.org/NMEICT-][http://spoken-tutorial.org/NMEICT-Intro Intro] ] <br /> <br /> |-<br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;&quot;| <br /> | style=&quot;background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;&quot;| This is Snehalatha from IIT Bombay signing off. Thank you for joining. <br /> <br /> |}</div>

Snehalathak