https://proteopedia.org/index.php?action=history&feed=atom&title=Calculate_structureCalculate structure - Revision history2026-10-04T06:16:18ZRevision history for this page on the wikiMediaWiki 1.43.8https://proteopedia.org/index.php?title=Calculate_structure&diff=1410606&oldid=prevKarl Oberholser at 15:25, 25 June 20122012-06-25T15:25:19Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* <scene name='Calculate_structure/Domain_2_3turns2/6'>High light</scene> each of the one residue T segments (''e.g.'' T : A:488_A:488) in the summary below along with a few residues on each side of the single residue. Improve the view by displaying these <scene name='Calculate_structure/Domain_2_3turns3/9'>segments in isolation</scene>. (Remember the hbonds can be displayed by running ''calculate hbonds structure'' from the console.) See summary below for a description of each of these T segments. All of these single residue segments are part of turns which are also involved in helices. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* <scene name='Calculate_structure/Domain_2_3turns2/6'>High light</scene> each of the one residue T segments (''e.g.'' T : A:488_A:488) in the summary below along with a few residues on each side of the single residue. Improve the view by displaying these <scene name='Calculate_structure/Domain_2_3turns3/9'>segments in isolation</scene>. (Remember the hbonds can be displayed by running ''calculate hbonds structure'' from the console.) See summary below for a description of each of these T segments. All of these single residue segments are part of turns which are also involved in helices. </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Reveal the nature of the <scene name='Calculate_structure/Domain_2_4turn/2'>remaining T segments</scene>. Displaying these <scene name='Calculate_structure/Domain_2_4turn2/<del style="font-weight: bold; text-decoration: none;">5</del>'>turns in isolation</scene> makes it easier to observe the hbonds. Inspecting them for hbonds (after running ''calculate hbonds structure'' from the console) reveals that all but one of these T segments are part of β-turns with the β-turns overlapping at two locations, and that segment T: 822-825 is part of a 4-turn and two 5-turns. <del style="font-weight: bold; text-decoration: none;">All but two of the segments have at least one residue colored blue (Nitrogens involved in hbonds are also colored blue for ease of identifying the atoms involved in the hbonds.). </del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Reveal the nature of the <scene name='Calculate_structure/Domain_2_4turn/2'>remaining T segments</scene>. Displaying these <scene name='Calculate_structure/Domain_2_4turn2/<ins style="font-weight: bold; text-decoration: none;">6</ins>'>turns in isolation</scene> makes it easier to observe the hbonds. Inspecting them for hbonds (after running ''calculate hbonds structure'' from the console) reveals that all but one of these T segments are part of β-turns with the β-turns overlapping at two locations, and that segment T: 822-825 is part of a 4-turn and two 5-turns. <ins style="font-weight: bold; text-decoration: none;"> </ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Summary of T's for Domain 2 of Chain A Glycogen Phosphorylase:'''(All other segments deleted.)<br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Summary of T's for Domain 2 of Chain A Glycogen Phosphorylase:'''(All other segments deleted.)<br></div></td></tr>
</table>Karl Oberholserhttps://proteopedia.org/index.php?title=Calculate_structure&diff=1410605&oldid=prevKarl Oberholser at 15:10, 25 June 20122012-06-25T15:10:56Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><scene name='Calculate_structure/Domain_2/5'>Load Structure</scene> <br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><scene name='Calculate_structure/Domain_2/5'>Load Structure</scene> <br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* <scene name='Calculate_structure/Domain_2_3turns2/<del style="font-weight: bold; text-decoration: none;">7</del>'>High light</scene> each of the one residue T segments (''e.g.'' T : A:488_A:488) in the summary below along with a few residues on each side of the single residue. Improve the view by displaying these <scene name='Calculate_structure/Domain_2_3turns3/<del style="font-weight: bold; text-decoration: none;">8</del>'>segments in isolation</scene>. (Remember <del style="font-weight: bold; text-decoration: none;">to display </del>the hbonds by running ''calculate hbonds structure'' from the console.) <del style="font-weight: bold; text-decoration: none;">Only one segment has a residue colored blue, and the other residues are colored as being part of a helix or sheet. </del>See summary below for a description of each of these T segments. All of these single residue segments are part of turns which are also involved in helices. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* <scene name='Calculate_structure/Domain_2_3turns2/<ins style="font-weight: bold; text-decoration: none;">6</ins>'>High light</scene> each of the one residue T segments (''e.g.'' T : A:488_A:488) in the summary below along with a few residues on each side of the single residue. Improve the view by displaying these <scene name='Calculate_structure/Domain_2_3turns3/<ins style="font-weight: bold; text-decoration: none;">9</ins>'>segments in isolation</scene>. (Remember the hbonds <ins style="font-weight: bold; text-decoration: none;">can be displayed </ins>by running ''calculate hbonds structure'' from the console.) See summary below for a description of each of these T segments. All of these single residue segments are part of turns which are also involved in helices. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Reveal the nature of the <scene name='Calculate_structure/Domain_2_4turn/2'>remaining T segments</scene>. Displaying these <scene name='Calculate_structure/Domain_2_4turn2/5'>turns in isolation</scene> makes it easier to observe the hbonds. Inspecting them for hbonds (after running ''calculate hbonds structure'' from the console) reveals that all but one of these T segments are part of β-turns with the β-turns overlapping at two locations, and that segment T: 822-825 is part of a 4-turn and two 5-turns. All but two of the segments have at least one residue colored blue (Nitrogens involved in hbonds are also colored blue for ease of identifying the atoms involved in the hbonds.). </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Reveal the nature of the <scene name='Calculate_structure/Domain_2_4turn/2'>remaining T segments</scene>. Displaying these <scene name='Calculate_structure/Domain_2_4turn2/5'>turns in isolation</scene> makes it easier to observe the hbonds. Inspecting them for hbonds (after running ''calculate hbonds structure'' from the console) reveals that all but one of these T segments are part of β-turns with the β-turns overlapping at two locations, and that segment T: 822-825 is part of a 4-turn and two 5-turns. All but two of the segments have at least one residue colored blue (Nitrogens involved in hbonds are also colored blue for ease of identifying the atoms involved in the hbonds.). </div></td></tr>
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</table>Karl Oberholserhttps://proteopedia.org/index.php?title=Calculate_structure&diff=1410395&oldid=prevKarl Oberholser at 20:25, 23 June 20122012-06-23T20:25:00Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><scene name='Calculate_structure/Domain_2/5'>Load Structure</scene> <br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><scene name='Calculate_structure/Domain_2/5'>Load Structure</scene> <br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* <scene name='Calculate_structure/Domain_2_3turns2/<del style="font-weight: bold; text-decoration: none;">6</del>'>High light</scene> each of the one residue T segments (''e.g.'' T : A:488_A:488) in the summary below along with a few residues on each side of the single residue. Improve the view by displaying these <scene name='Calculate_structure/Domain_2_3turns3/8'>segments in isolation</scene>. (Remember to display the hbonds by running ''calculate hbonds structure'' from the console.) Only one segment has a residue colored blue, and the other residues are colored as being part of a helix or sheet. See summary below for a description of each of these T segments. All of these single residue segments are part of turns which are also involved in helices. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* <scene name='Calculate_structure/Domain_2_3turns2/<ins style="font-weight: bold; text-decoration: none;">7</ins>'>High light</scene> each of the one residue T segments (''e.g.'' T : A:488_A:488) in the summary below along with a few residues on each side of the single residue. Improve the view by displaying these <scene name='Calculate_structure/Domain_2_3turns3/8'>segments in isolation</scene>. (Remember to display the hbonds by running ''calculate hbonds structure'' from the console.) Only one segment has a residue colored blue, and the other residues are colored as being part of a helix or sheet. See summary below for a description of each of these T segments. All of these single residue segments are part of turns which are also involved in helices. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Reveal the nature of the <scene name='Calculate_structure/Domain_2_4turn/2'>remaining T segments</scene>. Displaying these <scene name='Calculate_structure/Domain_2_4turn2/5'>turns in isolation</scene> makes it easier to observe the hbonds. Inspecting them for hbonds (after running ''calculate hbonds structure'' from the console) reveals that all but one of these T segments are part of β-turns with the β-turns overlapping at two locations, and that segment T: 822-825 is part of a 4-turn and two 5-turns. All but two of the segments have at least one residue colored blue (Nitrogens involved in hbonds are also colored blue for ease of identifying the atoms involved in the hbonds.). </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Reveal the nature of the <scene name='Calculate_structure/Domain_2_4turn/2'>remaining T segments</scene>. Displaying these <scene name='Calculate_structure/Domain_2_4turn2/5'>turns in isolation</scene> makes it easier to observe the hbonds. Inspecting them for hbonds (after running ''calculate hbonds structure'' from the console) reveals that all but one of these T segments are part of β-turns with the β-turns overlapping at two locations, and that segment T: 822-825 is part of a 4-turn and two 5-turns. All but two of the segments have at least one residue colored blue (Nitrogens involved in hbonds are also colored blue for ease of identifying the atoms involved in the hbonds.). </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
</table>Karl Oberholserhttps://proteopedia.org/index.php?title=Calculate_structure&diff=1410387&oldid=prevKarl Oberholser at 19:54, 21 June 20122012-06-21T19:54:27Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:54, 21 June 2012</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Domain 2 of chain A Glycogen Phosphorylase ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Domain 2 of chain A Glycogen Phosphorylase ===</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><scene name='Calculate_structure/Domain_2/5'>Load Structure</scene> <br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><scene name='Calculate_structure/Domain_2/5'>Load Structure</scene> <br></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">If the applet is not running the signed ver. 12 of Jmol, connect with it as you did above, and then click on the above green link.<br></del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">After clicking on the above green link, open the console and run the script: <center>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</center><br></del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* <scene name='Calculate_structure/Domain_2_3turns2/6'>High light</scene> each of the one residue T segments (''e.g.'' T : A:488_A:488) in the summary below along with a few residues on each side of the single residue. Improve the view by displaying these <scene name='Calculate_structure/Domain_2_3turns3/8'>segments in isolation</scene>. (Remember to display the hbonds by running ''calculate hbonds structure'' from the console.) Only one segment has a residue colored blue, and the other residues are colored as being part of a helix or sheet. See summary below for a description of each of these T segments. <ins style="font-weight: bold; text-decoration: none;">All of </ins>these single residue segments are part of <ins style="font-weight: bold; text-decoration: none;">turns which </ins>are <ins style="font-weight: bold; text-decoration: none;">also </ins>involved <ins style="font-weight: bold; text-decoration: none;">in </ins>helices. </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* <scene name='Calculate_structure/Domain_2_3turns2/6'>High light</scene> each of the one residue T segments (''e.g.'' T : A:488_A:488) in the summary below along with a few residues on each side of the single residue. Improve the view by displaying these <scene name='Calculate_structure/Domain_2_3turns3/8'>segments in isolation</scene>. (Remember to display the hbonds by running ''calculate hbonds structure'' from the console.) Only one segment has a residue colored blue, and the other residues are colored as being part of a helix or sheet. See summary below for a description of each of these T segments. <del style="font-weight: bold; text-decoration: none;">The only turns that </del>these single residue segments are part of are involved helices. </div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Reveal the nature of the <scene name='Calculate_structure/Domain_2_4turn/2'>remaining T segments</scene>. Displaying these <scene name='Calculate_structure/Domain_2_4turn2/5'>turns in isolation</scene> makes it easier to observe the hbonds. Inspecting them for hbonds (after running ''calculate hbonds structure'' from the console) reveals that all but one of these T segments are part of β-turns with the β-turns overlapping at two locations, and that segment T: 822-825 is part of a 4-turn and two 5-turns. All but two of the segments have at least one residue colored blue (Nitrogens involved in hbonds are also colored blue for ease of identifying the atoms involved in the hbonds.). </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Reveal the nature of the <scene name='Calculate_structure/Domain_2_4turn/2'>remaining T segments</scene>. Displaying these <scene name='Calculate_structure/Domain_2_4turn2/5'>turns in isolation</scene> makes it easier to observe the hbonds. Inspecting them for hbonds (after running ''calculate hbonds structure'' from the console) reveals that all but one of these T segments are part of β-turns with the β-turns overlapping at two locations, and that segment T: 822-825 is part of a 4-turn and two 5-turns. All but two of the segments have at least one residue colored blue (Nitrogens involved in hbonds are also colored blue for ease of identifying the atoms involved in the hbonds.). </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
</table>Karl Oberholserhttps://proteopedia.org/index.php?title=Calculate_structure&diff=1410386&oldid=prevKarl Oberholser at 19:37, 21 June 20122012-06-21T19:37:03Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:37, 21 June 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l39">Line 39:</td>
<td colspan="2" class="diff-lineno">Line 39:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* There are two T segments that contain one residue, <scene name='Calculate_structure/Turn_84/2'>T : A:86_A:86</scene> (β-turn 84-87; 84 & 85 are part of a helix, 86 is colored blue & 87 is white.) and <scene name='Calculate_structure/Turn_110/6'>T : A:110_A:110</scene> (β-turn 110-113; 110 is blue, 111-113 are part of a 3<sub>10</sub>-helix.). </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* There are two T segments that contain one residue, <scene name='Calculate_structure/Turn_84/2'>T : A:86_A:86</scene> (β-turn 84-87; 84 & 85 are part of a helix, 86 is colored blue & 87 is white.) and <scene name='Calculate_structure/Turn_110/6'>T : A:110_A:110</scene> (β-turn 110-113; 110 is blue, 111-113 are part of a 3<sub>10</sub>-helix.). </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* There are two T segments that contain two residues, <scene name='Calculate_structure/Turn_63/4'>T : A:65_A:66</scene> (β-turn 63-66; 63 & 64 part of a helix, 65 & 66 are blue.) and <scene name='Calculate_structure/Turn_67/7'>T : A:68_A:69</scene> (β-turn 67-70; 70 is part of a helix, 67 & 68 are white & blue, 69 entirely blue.).</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* There are two T segments that contain two residues, <scene name='Calculate_structure/Turn_63/4'>T : A:65_A:66</scene> (β-turn 63-66; 63 & 64 part of a helix, 65 & 66 are blue.) and <scene name='Calculate_structure/Turn_67/7'>T : A:68_A:69</scene> (β-turn 67-70; 70 is part of a helix, 67 & 68 are white & blue, 69 entirely blue.).</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* The last T is a three residue segment, <scene name='Calculate_structure/Turn_114/<del style="font-weight: bold; text-decoration: none;">2</del>'>T : A:115_A:117</scene> (β-turn 114-117, 4-turn 114-118; 114 is part of a 3<sub>10</sub>-helix, 115-117 & part of 118 are blue, 118 is partially white.). A β-turn is nested in a 4-turn.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* The last T is a three residue segment, <scene name='Calculate_structure/Turn_114/<ins style="font-weight: bold; text-decoration: none;">3</ins>'>T : A:115_A:117</scene> (β-turn 114-117, 4-turn 114-118; 114 is part of a 3<sub>10</sub>-helix, 115-117 & part of 118 are blue, 118 is partially white.). A β-turn is nested in a 4-turn.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Can you locate the two turns that are not colored with blue traces and do not contain a hbond between the first and the last residues of the turn. There are two class VIb β-turns in myohemerytherin.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Can you locate the two turns that are not colored with blue traces and do not contain a hbond between the first and the last residues of the turn. There are two class VIb β-turns in myohemerytherin.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l53">Line 53:</td>
<td colspan="2" class="diff-lineno">Line 53:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>T : A:110_A:110 &nbsp;&nbsp;<scene name='Calculate_structure/Turn_110/6'>Display beta-turn</scene><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>T : A:110_A:110 &nbsp;&nbsp;<scene name='Calculate_structure/Turn_110/6'>Display beta-turn</scene><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>G : A:111_A:114<br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>G : A:111_A:114<br></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>T : A:115_A:117 &nbsp;&nbsp;<scene name='Calculate_structure/Turn_114/<del style="font-weight: bold; text-decoration: none;">2</del>'>Display turns</scene><br></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>T : A:115_A:117 &nbsp;&nbsp;<scene name='Calculate_structure/Turn_114/<ins style="font-weight: bold; text-decoration: none;">3</ins>'>Display turns</scene><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Key - '''H''': α-helix; '''B''': β-bridge; '''E''': β-strand; '''G''': 3<sub>10</sub>-helix; '''I''': π-helix; '''T''': 3-, 4-, 5-turn; '''S''': bend.<br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Key - '''H''': α-helix; '''B''': β-bridge; '''E''': β-strand; '''G''': 3<sub>10</sub>-helix; '''I''': π-helix; '''T''': 3-, 4-, 5-turn; '''S''': bend.<br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Identify turns using resourses at RCSB ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Identify turns using resourses at RCSB ===</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>There are two resources at RCSB Protein Data Bank<ref name="RCSB">[http://www.pdb.org/pdb/home/home.do Open home page of PDB]</ref> that can be useful when analyzing the turns or any secondary structures of a protein. After going to the PDB site and selecting your protein of interest by entering the PDB ID or name of the protein, click on the Sequence tab. First one, clicking on 'Sequence & DSSP' under the Chain A heading opens in a separate window the sequence and secodary structures of chain A of the protein. Second one, in the 'Sequence & Structure Relationships' box click on 'Enable Jmol to view annotations in 3D' and then 'Display Jmol'. The Jmol applet remains on top as you scroll down to the annotated sequence. Clicking on a secondary structure in the DSSP bar results in that structure being high lighted in the Jmol applet. The turns that are identified as having only one residue are not shown on the DSSP bar, but if you hoover the cursor over the DSSP bar in the area of that one residue a label will appear identifying the turn, and then if you click the mouse the one residue turn will appear in the Jmol applet. If secondary structure annotations other than DSSP are used, β-turns classes VIa1, VIa2, and VIb may be identified, see myohemerytherin <del style="font-weight: bold; text-decoration: none;">below</del>. If you select one of the other annotations of secondary structure, you will discover that class VIb β-turns are among the structures being annotated. Use end note to open necessary sites.<ref>[http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=2MHR&params.showJmol=true Open myohemerytherin at sequence page with Jmol open]; &nbsp;&nbsp;[http://www.pdb.org/pdb/explore/sequenceText.do?structureId=2MHR&chainId=A Open sequence and Secondary structure page]</ref> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>There are two resources at RCSB Protein Data Bank<ref name="RCSB">[http://www.pdb.org/pdb/home/home.do Open home page of PDB]</ref> that can be useful when analyzing the turns or any secondary structures of a protein. After going to the PDB site and selecting your protein of interest by entering the PDB ID or name of the protein, click on the Sequence tab. First one, clicking on 'Sequence & DSSP' under the Chain A heading opens in a separate window the sequence and secodary structures of chain A of the protein. Second one, in the 'Sequence & Structure Relationships' box click on 'Enable Jmol to view annotations in 3D' and then 'Display Jmol'. The Jmol applet remains on top as you scroll down to the annotated sequence. Clicking on a secondary structure in the DSSP bar results in that structure being high lighted in the Jmol applet. The turns that are identified as having only one residue are not shown on the DSSP bar, but if you hoover the cursor over the DSSP bar in the area of that one residue a label will appear identifying the turn, and then if you click the mouse the one residue turn will appear in the Jmol applet. If secondary structure annotations other than DSSP are used, β-turns classes VIa1, VIa2, and VIb may be identified, see myohemerytherin <ins style="font-weight: bold; text-decoration: none;">above</ins>. If you select one of the other annotations of secondary structure, you will discover that class VIb β-turns are among the structures being annotated. Use end note to open necessary sites.<ref>[http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=2MHR&params.showJmol=true Open myohemerytherin at sequence page with Jmol open]; &nbsp;&nbsp;[http://www.pdb.org/pdb/explore/sequenceText.do?structureId=2MHR&chainId=A Open sequence and Secondary structure page]</ref> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Domain 2 of chain A Glycogen Phosphorylase ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Domain 2 of chain A Glycogen Phosphorylase ===</div></td></tr>
</table>Karl Oberholserhttps://proteopedia.org/index.php?title=Calculate_structure&diff=1410385&oldid=prevKarl Oberholser at 19:26, 21 June 20122012-06-21T19:26:13Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:26, 21 June 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l38">Line 38:</td>
<td colspan="2" class="diff-lineno">Line 38:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Myohemerytherin''' (<scene name='Calculate_structure/Erythrin/2'>Restore initial scene</scene>) </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Myohemerytherin''' (<scene name='Calculate_structure/Erythrin/2'>Restore initial scene</scene>) </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* There are two T segments that contain one residue, <scene name='Calculate_structure/Turn_84/2'>T : A:86_A:86</scene> (β-turn 84-87; 84 & 85 are part of a helix, 86 is colored blue & 87 is white.) and <scene name='Calculate_structure/Turn_110/6'>T : A:110_A:110</scene> (β-turn 110-113; 110 is blue, 111-113 are part of a 3<sub>10</sub>-helix.). </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* There are two T segments that contain one residue, <scene name='Calculate_structure/Turn_84/2'>T : A:86_A:86</scene> (β-turn 84-87; 84 & 85 are part of a helix, 86 is colored blue & 87 is white.) and <scene name='Calculate_structure/Turn_110/6'>T : A:110_A:110</scene> (β-turn 110-113; 110 is blue, 111-113 are part of a 3<sub>10</sub>-helix.). </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* There are two T segments that contain two residues, <scene name='Calculate_structure/Turn_63/<del style="font-weight: bold; text-decoration: none;">3</del>'>T : A:65_A:66</scene> (β-turn 63-66; 63 & 64 part of a helix, 65 & 66 are blue.) and <scene name='Calculate_structure/Turn_67/<del style="font-weight: bold; text-decoration: none;">6</del>'>T : A:68_A:69</scene> (β-turn 67-70; 70 is part of a helix, 67 & 68 are white & blue, 69 entirely blue.).</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* There are two T segments that contain two residues, <scene name='Calculate_structure/Turn_63/<ins style="font-weight: bold; text-decoration: none;">4</ins>'>T : A:65_A:66</scene> (β-turn 63-66; 63 & 64 part of a helix, 65 & 66 are blue.) and <scene name='Calculate_structure/Turn_67/<ins style="font-weight: bold; text-decoration: none;">7</ins>'>T : A:68_A:69</scene> (β-turn 67-70; 70 is part of a helix, 67 & 68 are white & blue, 69 entirely blue.).</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The last T is a three residue segment, <scene name='Calculate_structure/Turn_114/2'>T : A:115_A:117</scene> (β-turn 114-117, 4-turn 114-118; 114 is part of a 3<sub>10</sub>-helix, 115-117 & part of 118 are blue, 118 is partially white.). A β-turn is nested in a 4-turn.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The last T is a three residue segment, <scene name='Calculate_structure/Turn_114/2'>T : A:115_A:117</scene> (β-turn 114-117, 4-turn 114-118; 114 is part of a 3<sub>10</sub>-helix, 115-117 & part of 118 are blue, 118 is partially white.). A β-turn is nested in a 4-turn.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Can you locate the two turns that are not colored with blue traces and do not contain a hbond between the first and the last residues of the turn. There are two class VIb β-turns in myohemerytherin.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Can you locate the two turns that are not colored with blue traces and do not contain a hbond between the first and the last residues of the turn. There are two class VIb β-turns in myohemerytherin.</div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>H : A:19_A:37<br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>H : A:19_A:37<br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>H : A:41_A:64 <br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>H : A:41_A:64 <br></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>T : A:65_A:66 &nbsp;&nbsp;<scene name='Calculate_structure/Turn_63/<del style="font-weight: bold; text-decoration: none;">3</del>'>Display beta-turn</scene><br></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>T : A:65_A:66 &nbsp;&nbsp;<scene name='Calculate_structure/Turn_63/<ins style="font-weight: bold; text-decoration: none;">4</ins>'>Display beta-turn</scene><br></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>T : A:68_A:69 &nbsp;&nbsp;<scene name='Calculate_structure/Turn_67/<del style="font-weight: bold; text-decoration: none;">6</del>'>Display beta-turn</scene>; <br></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>T : A:68_A:69 &nbsp;&nbsp;<scene name='Calculate_structure/Turn_67/<ins style="font-weight: bold; text-decoration: none;">7</ins>'>Display beta-turn</scene>; <br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>H : A:70_A:85<br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>H : A:70_A:85<br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>T : A:86_A:86 &nbsp;&nbsp;<scene name='Calculate_structure/Turn_84/2'>Display beta-turn</scene><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>T : A:86_A:86 &nbsp;&nbsp;<scene name='Calculate_structure/Turn_84/2'>Display beta-turn</scene><br></div></td></tr>
</table>Karl Oberholserhttps://proteopedia.org/index.php?title=Calculate_structure&diff=1410383&oldid=prevKarl Oberholser at 19:05, 21 June 20122012-06-21T19:05:08Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:05, 21 June 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l31">Line 31:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* All two-residue T segments indicate β-turns. The turns are often part of an helix, as many as three of the four residues can have the color of the helix. Isolated β-turns have two to three residues colored blue in the structure, rarely four. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* All two-residue T segments indicate β-turns. The turns are often part of an helix, as many as three of the four residues can have the color of the helix. Isolated β-turns have two to three residues colored blue in the structure, rarely four. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* T segments that have more than two residues indicate two contiguous or nested β-turns, β-turn nested in a 4- or 5-turn, isolated or nested 4 or 5-turns. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* T segments that have more than two residues indicate two contiguous or nested β-turns, β-turn nested in a 4- or 5-turn, isolated or nested 4 or 5-turns. </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* After ''calculate structure'' and ''calculate hbonds structure'' has been run the following methods can be used to identify the different types of turns. Blue coloration and the hbond bond between ''i'' and ''i'' + 3 can be used to identify overlapping and isolated β-turns. The 4- or 5-turns which are nested in some way are easily identified by residue ''i'' being involved in at least two hbonds. β-<del style="font-weight: bold; text-decoration: none;">turns </del>VIa1, VIa2, and VIb can be identified by locating a trace that has the appearance of a β-turns and is not colored blue and checking for a cis-Pro at ''i + 2''. (Hover the cursor over the trace to display the name and number of the residues.) Also, the values for phi and psi angles at ''i + 1'' and ''i + 2'' can be [[Psi and Phi Angles|determined]] and compared to the values expected for classes VIa1, VIa2, and VIb.<ref name=beta /></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* After ''calculate structure'' and ''calculate hbonds structure'' has been run the following methods can be used to identify the different types of turns. Blue coloration and the hbond bond between ''i'' and ''i'' + 3 can be used to identify overlapping and isolated β-turns. The 4- or 5-turns which are nested in some way are easily identified by residue ''i'' being involved in at least two hbonds. β-<ins style="font-weight: bold; text-decoration: none;">turn classes </ins>VIa1, VIa2, and VIb <ins style="font-weight: bold; text-decoration: none;">(Do not contain hydrogen bonds.) </ins>can be identified by locating a trace that has the appearance of a β-turns and is not colored blue and checking for a cis-Pro at ''i + 2''. (Hover the cursor over the trace to display the name and number of the residues.) Also, the values for phi and psi angles at ''i + 1'' and ''i + 2'' can be [[Psi and Phi Angles|determined]] and compared to the values expected for classes VIa1, VIa2, and VIb.<ref name=beta /></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Illustrations ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Illustrations ===</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">The user is urged to use the above directions to open Jmol version 12 and to run the ''calculate structure'' and the accompanying commands so that the resulting display can be compared with the summary below. Without displaying the images generated by ''calculate structure'' and ''calculate hbonds structure'' the activities and comparisons described below can not be performed. Unless a green link is designed to change the color and structural representation, these two display parameters do not change after they have been set by ''calculate structure'', but all </del>hbonds are deleted by clicking a green link <del style="font-weight: bold; text-decoration: none;">so </del>''calculate hbonds structure'' has to be run from the console after every green link click in order to display hbonds.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Since </ins>hbonds are deleted by clicking a <ins style="font-weight: bold; text-decoration: none;">subsequent </ins>green link<ins style="font-weight: bold; text-decoration: none;">, </ins>''calculate hbonds structure'' has to be run from the <ins style="font-weight: bold; text-decoration: none;">Jmol </ins>console<ins style="font-weight: bold; text-decoration: none;">, as described above, </ins>after every green link click in order to display hbonds<ins style="font-weight: bold; text-decoration: none;">. The display of hbonds can be helpful in identifying turns</ins>.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Myohemerytherin''' (<scene name='Calculate_structure/Erythrin/2'>Restore initial scene</scene>) </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Myohemerytherin''' (<scene name='Calculate_structure/Erythrin/2'>Restore initial scene</scene>) </div></td></tr>
</table>Karl Oberholserhttps://proteopedia.org/index.php?title=Calculate_structure&diff=1410377&oldid=prevKarl Oberholser at 18:17, 21 June 20122012-06-21T18:17:13Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:17, 21 June 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>An important part of protein structure is the [[secondary structure]] which is made up of [[Helices in Proteins|helices]], [[Sheets in Proteins|sheets]] and [[Turns in Proteins|turns]], and Jmol has always been capable of determining and displaying these three types of structures with limitations as described in [[Secondary_structure#How Jmol Determines Secondary Structure | How Jmol Determines Secondary Structure ]]. The ''calculate structure''<ref name="calculate">A detailed description is at [http://chemapps.stolaf.edu/jmol/docs/#calculate].</ref> is a command which has been more recently developed and does <del style="font-weight: bold; text-decoration: none;">a more detailed </del>identification of these secondary structures. <del style="font-weight: bold; text-decoration: none;">(For this detail go to [[Helices in Proteins|helices]], [[Sheets in Proteins|sheets]] and [[Turns in Proteins|turns]].) </del>Calculate structure by itself only identifies the secondary <del style="font-weight: bold; text-decoration: none;">structural components</del>. Additional commands are required to <del style="font-weight: bold; text-decoration: none;">display </del>the secondary structures and the hbonds. <del style="font-weight: bold; text-decoration: none;"> </del>In order to display <del style="font-weight: bold; text-decoration: none;">this detailed information on </del>any <del style="font-weight: bold; text-decoration: none;">Proteopedia page </del>which does not <del style="font-weight: bold; text-decoration: none;">display it</del>, click on the ''Jmol frank'', in the ''main menu'' click on ''Console'', in the bottom box of the console enter the <del style="font-weight: bold; text-decoration: none;">commands: </del><span style='background-color:yellow;'>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</span> <del style="font-weight: bold; text-decoration: none;">and then click ''Run''</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>An important part of protein structure is the [[secondary structure]] which is made up of [[Helices in Proteins|helices]], [[Sheets in Proteins|sheets]] and [[Turns in Proteins|turns]], and Jmol has always been capable of determining and displaying these three types of structures with limitations as described in [[Secondary_structure#How Jmol Determines Secondary Structure | How Jmol Determines Secondary Structure ]]. The ''calculate structure''<ref name="calculate">A detailed description is at [http://chemapps.stolaf.edu/jmol/docs/#calculate].</ref> is a command which has been more recently developed and does <ins style="font-weight: bold; text-decoration: none;">an objective </ins>identification of these secondary structures. <ins style="font-weight: bold; text-decoration: none;">''</ins>Calculate structure<ins style="font-weight: bold; text-decoration: none;">'' </ins>by itself only identifies the <ins style="font-weight: bold; text-decoration: none;">different </ins>secondary <ins style="font-weight: bold; text-decoration: none;">structures and does not result in the display of a structure</ins>. Additional commands are required to <ins style="font-weight: bold; text-decoration: none;">color and render </ins>the secondary structures <ins style="font-weight: bold; text-decoration: none;">differentially </ins>and <ins style="font-weight: bold; text-decoration: none;">to display </ins>the <ins style="font-weight: bold; text-decoration: none;">hydrogen bonds (hbonds). The development of the scenes in this article included the use of the script ''select protein; calculate structure; cartoon; color structure''. Since the post-green link processing of the ''calculate </ins>hbonds <ins style="font-weight: bold; text-decoration: none;">structure'' command is malfunctioning, it was not used when making the scenes</ins>. In order to display <ins style="font-weight: bold; text-decoration: none;">hbonds in </ins>any <ins style="font-weight: bold; text-decoration: none;">scene </ins>which does not <ins style="font-weight: bold; text-decoration: none;">show them</ins>, click on the ''Jmol frank'', in the ''main menu'' click on ''Console'', in the bottom box of the console enter the <ins style="font-weight: bold; text-decoration: none;">command ''calculate hbonds structure'' and then click ''Run''. This same technique, with the exception of entering </ins><span style='background-color:yellow;'>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</span> <ins style="font-weight: bold; text-decoration: none;">into the lower console box, can be used to do an objective identification of the secondary structures on any Proteopedia page in which it has not been done</ins>.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The objectives of this article are:</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The objectives of this article are:</div></td></tr>
</table>Karl Oberholserhttps://proteopedia.org/index.php?title=Calculate_structure&diff=1410375&oldid=prevKarl Oberholser at 16:36, 21 June 20122012-06-21T16:36:30Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:36, 21 June 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l37">Line 37:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Myohemerytherin''' (<scene name='Calculate_structure/Erythrin/2'>Restore initial scene</scene>) </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''Myohemerytherin''' (<scene name='Calculate_structure/Erythrin/2'>Restore initial scene</scene>) </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* There are two T segments that contain one residue, <scene name='Calculate_structure/Turn_84/2'>T : A:86_A:86</scene> (β-turn 84-87; 84 & 85 are part of a helix, 86 is colored blue & 87 is white.) and <scene name='Calculate_structure/Turn_110/<del style="font-weight: bold; text-decoration: none;">3</del>'>T : A:110_A:110</scene> (β-turn 110-113; 110 is blue, 111-113 are part of a 3<sub>10</sub>-helix.). </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* There are two T segments that contain one residue, <scene name='Calculate_structure/Turn_84/2'>T : A:86_A:86</scene> (β-turn 84-87; 84 & 85 are part of a helix, 86 is colored blue & 87 is white.) and <scene name='Calculate_structure/Turn_110/<ins style="font-weight: bold; text-decoration: none;">6</ins>'>T : A:110_A:110</scene> (β-turn 110-113; 110 is blue, 111-113 are part of a 3<sub>10</sub>-helix.). </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* There are two T segments that contain two residues, <scene name='Calculate_structure/Turn_63/3'>T : A:65_A:66</scene> (β-turn 63-66; 63 & 64 part of a helix, 65 & 66 are blue.) and <scene name='Calculate_structure/Turn_67/6'>T : A:68_A:69</scene> (β-turn 67-70; 70 is part of a helix, 67 & 68 are white & blue, 69 entirely blue.).</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* There are two T segments that contain two residues, <scene name='Calculate_structure/Turn_63/3'>T : A:65_A:66</scene> (β-turn 63-66; 63 & 64 part of a helix, 65 & 66 are blue.) and <scene name='Calculate_structure/Turn_67/6'>T : A:68_A:69</scene> (β-turn 67-70; 70 is part of a helix, 67 & 68 are white & blue, 69 entirely blue.).</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The last T is a three residue segment, <scene name='Calculate_structure/Turn_114/2'>T : A:115_A:117</scene> (β-turn 114-117, 4-turn 114-118; 114 is part of a 3<sub>10</sub>-helix, 115-117 & part of 118 are blue, 118 is partially white.). A β-turn is nested in a 4-turn.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The last T is a three residue segment, <scene name='Calculate_structure/Turn_114/2'>T : A:115_A:117</scene> (β-turn 114-117, 4-turn 114-118; 114 is part of a 3<sub>10</sub>-helix, 115-117 & part of 118 are blue, 118 is partially white.). A β-turn is nested in a 4-turn.</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l51">Line 51:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>T : A:86_A:86 &nbsp;&nbsp;<scene name='Calculate_structure/Turn_84/2'>Display beta-turn</scene><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>T : A:86_A:86 &nbsp;&nbsp;<scene name='Calculate_structure/Turn_84/2'>Display beta-turn</scene><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>H : A:93_A:109<br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>H : A:93_A:109<br></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>T : A:110_A:110 &nbsp;&nbsp;<scene name='Calculate_structure/Turn_110/<del style="font-weight: bold; text-decoration: none;">2</del>'>Display beta-turn</scene><br></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>T : A:110_A:110 &nbsp;&nbsp;<scene name='Calculate_structure/Turn_110/<ins style="font-weight: bold; text-decoration: none;">6</ins>'>Display beta-turn</scene><br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>G : A:111_A:114<br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>G : A:111_A:114<br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>T : A:115_A:117 &nbsp;&nbsp;<scene name='Calculate_structure/Turn_114/2'>Display turns</scene><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>T : A:115_A:117 &nbsp;&nbsp;<scene name='Calculate_structure/Turn_114/2'>Display turns</scene><br></div></td></tr>
</table>Karl Oberholserhttps://proteopedia.org/index.php?title=Calculate_structure&diff=1410366&oldid=prevKarl Oberholser at 15:23, 21 June 20122012-06-21T15:23:53Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:23, 21 June 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l60">Line 60:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Domain 2 of chain A Glycogen Phosphorylase ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Domain 2 of chain A Glycogen Phosphorylase ===</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><scene name='Calculate_structure/Domain_2/<del style="font-weight: bold; text-decoration: none;">2</del>'>Load Structure</scene> <br></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><scene name='Calculate_structure/Domain_2/<ins style="font-weight: bold; text-decoration: none;">5</ins>'>Load Structure</scene> <br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>If the applet is not running the signed ver. 12 of Jmol, connect with it as you did above, and then click on the above green link.<br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>If the applet is not running the signed ver. 12 of Jmol, connect with it as you did above, and then click on the above green link.<br></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>After clicking on the above green link, open the console and run the script: <center>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</center><br></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>After clicking on the above green link, open the console and run the script: <center>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</center><br></div></td></tr>
</table>Karl Oberholser