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Talk:Alpha helix
From Proteopedia
(Difference between revisions)
(New page: ==List of figure== --~~~~ ===Initial view=== script: https://proteopedia.org/wiki/scripts/77/778341/Ballstick/1.spt coords: https://proteopedia.org/cgi-bin/getfrozenstructure?abb78d56d3e0...) |
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| - | ==List of | + | ==List of figures: Alpha_helix== |
| - | --[[User:Karsten Theis|Karsten Theis]] | + | |
| + | --[[User:Karsten Theis|Karsten Theis]] 15:21, 3 September 2020 (UTC) | ||
| + | |||
===Initial view=== | ===Initial view=== | ||
script: https://proteopedia.org/wiki/scripts/77/778341/Ballstick/1.spt | script: https://proteopedia.org/wiki/scripts/77/778341/Ballstick/1.spt | ||
| + | Available on this page: User:Karsten_Theis/alpha_helix | ||
coords: https://proteopedia.org/cgi-bin/getfrozenstructure?abb78d56d3e07a4e0290a8783dcb8b58 | coords: https://proteopedia.org/cgi-bin/getfrozenstructure?abb78d56d3e07a4e0290a8783dcb8b58 | ||
| Line 9: | Line 12: | ||
===alpha helix=== | ===alpha helix=== | ||
script: https://proteopedia.org/wiki/scripts/77/778341/Ballstick/2.spt | script: https://proteopedia.org/wiki/scripts/77/778341/Ballstick/2.spt | ||
| + | Available on this page: Alpha_helix | ||
coords: same as Initial view | coords: same as Initial view | ||
| Line 15: | Line 19: | ||
===right-handed helix=== | ===right-handed helix=== | ||
script: https://proteopedia.org/wiki/scripts/77/778341/Ribbon/1.spt | script: https://proteopedia.org/wiki/scripts/77/778341/Ribbon/1.spt | ||
| + | Available on this page: User:Karsten_Theis/alpha_helix | ||
coords: same as Initial view | coords: same as Initial view | ||
| Line 21: | Line 26: | ||
===hydrogen bonds=== | ===hydrogen bonds=== | ||
script: https://proteopedia.org/wiki/scripts/77/778341/Hbonds/2.spt | script: https://proteopedia.org/wiki/scripts/77/778341/Hbonds/2.spt | ||
| + | Available on this page: User:Karsten_Theis/alpha_helix | ||
coords: same as Initial view | coords: same as Initial view | ||
| Line 27: | Line 33: | ||
===3.6 residues per turn=== | ===3.6 residues per turn=== | ||
script: https://proteopedia.org/wiki/scripts/77/778341/Wheel/1.spt | script: https://proteopedia.org/wiki/scripts/77/778341/Wheel/1.spt | ||
| + | Available on this page: User:Karsten_Theis/alpha_helix | ||
coords: same as Initial view | coords: same as Initial view | ||
| Line 33: | Line 40: | ||
===kink in a helix=== | ===kink in a helix=== | ||
script: https://proteopedia.org/wiki/scripts/77/778341/Proline/4.spt | script: https://proteopedia.org/wiki/scripts/77/778341/Proline/4.spt | ||
| + | Available on this page: Alpha_helix | ||
coords: https://proteopedia.org/cgi-bin/getfrozenstructure?edfb4ce39cfe73bccb63eb7f6261b144 | coords: https://proteopedia.org/cgi-bin/getfrozenstructure?edfb4ce39cfe73bccb63eb7f6261b144 | ||
| Line 39: | Line 47: | ||
===proline=== | ===proline=== | ||
script: https://proteopedia.org/wiki/scripts/77/778341/Proline/5.spt | script: https://proteopedia.org/wiki/scripts/77/778341/Proline/5.spt | ||
| + | Available on this page: Alpha_helix | ||
coords: same as kink in a helix | coords: same as kink in a helix | ||
| Line 45: | Line 54: | ||
===the helix in crambin=== | ===the helix in crambin=== | ||
script: https://proteopedia.org/wiki/scripts/77/778341/Proline_cap/1.spt | script: https://proteopedia.org/wiki/scripts/77/778341/Proline_cap/1.spt | ||
| + | Available on this page: User:Karsten_Theis/alpha_helix | ||
coords: https://proteopedia.org/cgi-bin/getfrozenstructure?9366550c976e80068b9dc9648aff81c5 | coords: https://proteopedia.org/cgi-bin/getfrozenstructure?9366550c976e80068b9dc9648aff81c5 | ||
| Line 51: | Line 61: | ||
===C-terminal end=== | ===C-terminal end=== | ||
script: https://proteopedia.org/wiki/scripts/77/778341/Proline_cap_detail/2.spt | script: https://proteopedia.org/wiki/scripts/77/778341/Proline_cap_detail/2.spt | ||
| + | Available on this page: User:Karsten_Theis/alpha_helix | ||
coords: same as the helix in crambin | coords: same as the helix in crambin | ||
| Line 56: | Line 67: | ||
===Jmol commands: buttons etc=== | ===Jmol commands: buttons etc=== | ||
====side chains==== | ====side chains==== | ||
| - | + | select 6-14:A and sidechain; spacefill 20%; wireframe 0.3; delay 0.8; select 4-16:A and backbone or 4-16:A.CB; restrict selected;\n | |
====ON==== | ====ON==== | ||
| - | + | stereo 5\n | |
====OFF==== | ====OFF==== | ||
| - | + | stereo off\n | |
====carbonyl oxygen==== | ====carbonyl oxygen==== | ||
| - | + | select 6-10:A.O; spacefill 30%; delay 0.4; spacefill 20%; delay 0.4; spacefill 30%; delay 0.4; spacefill 20%l delay 0.4;\n | |
====amino group==== | ====amino group==== | ||
| - | + | select 10-14:A.N; spacefill 30%; delay 0.4; spacefill 20%; delay 0.4; spacefill 30%; delay 0.4; spacefill 20%l delay 0.4;\n | |
====increase the sphere radii==== | ====increase the sphere radii==== | ||
| - | + | select visible; spacefill 30%; delay 0.2; spacefill 40%; delay 0.2; spacefill 50%; delay 0.2; spacefill 60%; delay 0.2; spacefill 70%; delay 0.2; spacefill 80%; delay 0.2; spacefill 90%; delay 0.2; spacefill 100%; delay 1.8; spacefill 20%;\n | |
====phi and psi==== | ====phi and psi==== | ||
| - | + | select 9-12:A; draw rama; restrict selected; restrict backbone; hbonds off\n | |
====show helical axes with rockets==== | ====show helical axes with rockets==== | ||
| - | + | select 58-61:A; structure turn; select 50-58:A; rockets on; select 60-69:A; rockets on;\n | |
===Summary=== | ===Summary=== | ||
| - | Total of green links: 9 | + | Total of green links: 9 |
| + | |||
| + | Total of Jmol buttons etc: 8 | ||
====coordinates used==== | ====coordinates used==== | ||
| - | */cgi-bin/getfrozenstructure?abb78d56d3e07a4e0290a8783dcb8b58 | + | *do a manual check: https://proteopedia.org/cgi-bin/getfrozenstructure?abb78d56d3e07a4e0290a8783dcb8b58 |
| - | */cgi-bin/getfrozenstructure?edfb4ce39cfe73bccb63eb7f6261b144 | + | *1FIA: https://proteopedia.org/cgi-bin/getfrozenstructure?edfb4ce39cfe73bccb63eb7f6261b144 |
| - | */cgi-bin/getfrozenstructure?9366550c976e80068b9dc9648aff81c5 | + | *3NIR: https://proteopedia.org/cgi-bin/getfrozenstructure?9366550c976e80068b9dc9648aff81c5 |
| + | ==3D scenes== | ||
| + | <StructureSection load='' size='350' side='right' caption='' scene=''><scene name='77/778341/Ballstick/1'>77/778341/Ballstick/1</scene> | ||
| + | |||
| + | <scene name='77/778341/Ballstick/2'>77/778341/Ballstick/2</scene> | ||
| + | |||
| + | <scene name='77/778341/Ribbon/1'>77/778341/Ribbon/1</scene> | ||
| + | |||
| + | <scene name='77/778341/Hbonds/2'>77/778341/Hbonds/2</scene> | ||
| + | |||
| + | <scene name='77/778341/Wheel/1'>77/778341/Wheel/1</scene> | ||
| + | |||
| + | <scene name='77/778341/Proline/4'>77/778341/Proline/4</scene> | ||
| + | |||
| + | <scene name='77/778341/Proline/5'>77/778341/Proline/5</scene> | ||
| + | |||
| + | <scene name='77/778341/Proline_cap/1'>77/778341/Proline_cap/1</scene> | ||
| + | |||
| + | <scene name='77/778341/Proline_cap_detail/2'>77/778341/Proline_cap_detail/2</scene> | ||
| + | </StructureSection> | ||
Current revision
Contents |
List of figures: Alpha_helix
--Karsten Theis 15:21, 3 September 2020 (UTC)
Initial view
script: https://proteopedia.org/wiki/scripts/77/778341/Ballstick/1.spt Available on this page: User:Karsten_Theis/alpha_helix
coords: https://proteopedia.org/cgi-bin/getfrozenstructure?abb78d56d3e07a4e0290a8783dcb8b58
alpha helix
script: https://proteopedia.org/wiki/scripts/77/778341/Ballstick/2.spt Available on this page: Alpha_helix
coords: same as Initial view
right-handed helix
script: https://proteopedia.org/wiki/scripts/77/778341/Ribbon/1.spt Available on this page: User:Karsten_Theis/alpha_helix
coords: same as Initial view
hydrogen bonds
script: https://proteopedia.org/wiki/scripts/77/778341/Hbonds/2.spt Available on this page: User:Karsten_Theis/alpha_helix
coords: same as Initial view
3.6 residues per turn
script: https://proteopedia.org/wiki/scripts/77/778341/Wheel/1.spt Available on this page: User:Karsten_Theis/alpha_helix
coords: same as Initial view
kink in a helix
script: https://proteopedia.org/wiki/scripts/77/778341/Proline/4.spt Available on this page: Alpha_helix
coords: https://proteopedia.org/cgi-bin/getfrozenstructure?edfb4ce39cfe73bccb63eb7f6261b144
proline
script: https://proteopedia.org/wiki/scripts/77/778341/Proline/5.spt Available on this page: Alpha_helix
coords: same as kink in a helix
the helix in crambin
script: https://proteopedia.org/wiki/scripts/77/778341/Proline_cap/1.spt Available on this page: User:Karsten_Theis/alpha_helix
coords: https://proteopedia.org/cgi-bin/getfrozenstructure?9366550c976e80068b9dc9648aff81c5
C-terminal end
script: https://proteopedia.org/wiki/scripts/77/778341/Proline_cap_detail/2.spt Available on this page: User:Karsten_Theis/alpha_helix
coords: same as the helix in crambin
Jmol commands: buttons etc
side chains
select 6-14:A and sidechain; spacefill 20%; wireframe 0.3; delay 0.8; select 4-16:A and backbone or 4-16:A.CB; restrict selected;\n
ON
stereo 5\n
OFF
stereo off\n
carbonyl oxygen
select 6-10:A.O; spacefill 30%; delay 0.4; spacefill 20%; delay 0.4; spacefill 30%; delay 0.4; spacefill 20%l delay 0.4;\n
amino group
select 10-14:A.N; spacefill 30%; delay 0.4; spacefill 20%; delay 0.4; spacefill 30%; delay 0.4; spacefill 20%l delay 0.4;\n
increase the sphere radii
select visible; spacefill 30%; delay 0.2; spacefill 40%; delay 0.2; spacefill 50%; delay 0.2; spacefill 60%; delay 0.2; spacefill 70%; delay 0.2; spacefill 80%; delay 0.2; spacefill 90%; delay 0.2; spacefill 100%; delay 1.8; spacefill 20%;\n
phi and psi
select 9-12:A; draw rama; restrict selected; restrict backbone; hbonds off\n
show helical axes with rockets
select 58-61:A; structure turn; select 50-58:A; rockets on; select 60-69:A; rockets on;\n
Summary
Total of green links: 9
Total of Jmol buttons etc: 8
coordinates used
- do a manual check: https://proteopedia.org/cgi-bin/getfrozenstructure?abb78d56d3e07a4e0290a8783dcb8b58
- 1FIA: https://proteopedia.org/cgi-bin/getfrozenstructure?edfb4ce39cfe73bccb63eb7f6261b144
- 3NIR: https://proteopedia.org/cgi-bin/getfrozenstructure?9366550c976e80068b9dc9648aff81c5
3D scenes
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