Calculate structure: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| Line 66: | Line 66: | ||
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> | 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 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. The only turns that these single residue segments are part of are involved helices. | * <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. The only turns that these single residue segments are part of are involved helices. | ||
* 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 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.). | * 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.). | ||
'''Summary of T's for Domain 2 of Chain A Glycogen Phosphorylase:'''(All other segments deleted.)<br> | '''Summary of T's for Domain 2 of Chain A Glycogen Phosphorylase:'''(All other segments deleted.)<br> | ||
T : A:488_A:488 488 (colored blue) is between a sheet & 3<sub>10</sub>-helix.<br> | T : A:488_A:488 488 (colored blue) is between a sheet & 3<sub>10</sub>-helix.<br> | ||
T : A:495_A:495 495 is at the end of α-helix.<br> | T : A:495_A:495 495 is at the end of α-helix.<br> | ||
T : A:525_A:526 β-turn 524-527; | T : A:525_A:526 β-turn 524-527; first three residues are part of a helix with 527 partially colored blue.<br> | ||
T : A:594_A:595 β-turn 593-596; 594 & 595 are colored blue, 593 is end of a sheet.<br> | T : A:594_A:595 β-turn 593-596; 594 & 595 are colored blue, 593 is end of a sheet.<br> | ||
T : A:611_A:612 β-turn 610-613; 611 & 612 are colored blue, other two are white.<br> | T : A:611_A:612 β-turn 610-613; 611 & 612 are colored blue, other two are white.<br> | ||
| Line 87: | Line 87: | ||
T : A:822_A:825 5-turns at 820-825 & 821-826; 822-824 are part of helix, 825 is blue, 826 is white.<br> | T : A:822_A:825 5-turns at 820-825 & 821-826; 822-824 are part of helix, 825 is blue, 826 is white.<br> | ||
=== Identify turns using resourses at RCSB === | |||
</StructureSection> | </StructureSection> | ||
