Calculate structure: Difference between revisions

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'''Domain 2 of chain A Glycogen Phosphorylase''' (<scene name='Calculate_structure/Domain_2/2'>Load Structure</scene>) - 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>

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>

* <scene name='Calculate_structure/Domain_2_3turns2/6'>High ~~lite~~</scene> ~~each~~ of the one residue T segments (''e.g.'' T : A:488_A:488) in the summary below along with some residues on each side of each single residue. (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~~. Improve the view by displaying these <scene name='Calculate_structure/Domain_2_3turns3/8'>segments in isolation</scene>~~. See summary below for a description of each of these T: segments.

* <scene name='Calculate_structure/Domain_2_3turns2/6'>High light</scene> all of the one residue T segments (''e.g.'' T : A:488_A:488) in the summary below along with some residues on each side of each 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. None of the residues labeled with T: on the summary are part of an isolated turn. Those involved in turns are part of a helix.

* Reveal the nature of the <scene name='Calculate_structure/Domain_2_4turn/2'>remaining T segments</scene>. 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, and that segment (822-825) is part of a 4-turn and two 5-turns~~. Displaying these <scene name='Calculate_structure/Domain_2_4turn2/5'>turns in isolation</scene> makes it easier to observe the hbonds~~. Using the residue numbers in the summary one can determine which residues make up the turns. At two places the β-turns overlap. 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 hbonds.).

* 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, and that segment (822-825) is part of a 4-turn and two 5-turns. Using the residue numbers in the summary one can determine which residues make up the turns. At two places the β-turns overlap. 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 hbonds.).

* Are there any β-turns that do not have hbonds but do have a Pro at position 3?

Calculate structure: Difference between revisions

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 '''Domain 2 of chain A Glycogen Phosphorylase''' (<scene name='Calculate_structure/Domain_2/2'>Load Structure</scene>) - 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>
 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>
-* <scene name='Calculate_structure/Domain_2_3turns2/6'>High lite</scene> each of the one residue T segments (''e.g.'' T : A:488_A:488) in the summary below along with some residues on each side of each single residue. (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. Improve the view by displaying these <scene name='Calculate_structure/Domain_2_3turns3/8'>segments in isolation</scene>. See summary below for a description of each of these T: segments.
+* <scene name='Calculate_structure/Domain_2_3turns2/6'>High light</scene> all of the one residue T segments (''e.g.'' T : A:488_A:488) in the summary below along with some residues on each side of each 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. None of the residues labeled with T: on the summary are part of an isolated turn. Those involved in turns are part of a helix.
-* Reveal the nature of the <scene name='Calculate_structure/Domain_2_4turn/2'>remaining T segments</scene>. 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, and that segment (822-825) is part of a 4-turn and two 5-turns. Displaying these <scene name='Calculate_structure/Domain_2_4turn2/5'>turns in isolation</scene> makes it easier to observe the hbonds. Using the residue numbers in the summary one can determine which residues make up the turns. At two places the β-turns overlap.  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 hbonds.).
+* 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, and that segment (822-825) is part of a 4-turn and two 5-turns. Using the residue numbers in the summary one can determine which residues make up the turns. At two places the β-turns overlap.  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 hbonds.).
 * Are there any β-turns that do not have hbonds but do have a Pro at position 3?