Ramachandran Plot: Difference between revisions

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<scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_planes/2'>Draw planes </scene> of two peptide bonds. The <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_halos_psi/6'>four atoms </scene>making up ψ remain translucent, and the remaining atoms become transparent. After rotating the structure so that ~~the four atoms~~ can be clearly ~~seen~~, determine and display the numerical value of ψ by double clicking on a nitrogen of the peptide bond, single clicking on the next two atoms and then double clicking on the second nitrogen. (If the structure rotates in the course of clicking on the atoms or if you encounter some other problem, re-click on the green link 'four atoms' and restart the clicking on the atoms.) The <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_halos_phi/5'>four atoms</scene> making up φ remain translucent, and the remaining atoms become transparent. After rotating the structure so that the four atoms can be clearly seen, measure and display the numerical value of φ using the technique described above. <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_draw_rama/5'>Confirm</scene> the direction of rotation and the values of ψ and φ.

<scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_planes/2'>Draw planes </scene> of two peptide bonds. The <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_halos_psi/6'>four atoms </scene>making up ψ remain translucent, and the remaining atoms become transparent. After rotating the structure so that you can clearly see that you are not clicking on a transparent atom, determine and display the numerical value of ψ by double clicking on a nitrogen of the peptide bond, single clicking on the next two atoms and then double clicking on the second nitrogen. (If the structure rotates in the course of clicking on the atoms or if you encounter some other problem, re-click on the green link 'four atoms' and restart the clicking on the atoms.) The <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_halos_phi/5'>four atoms</scene> making up φ remain translucent, and the remaining atoms become transparent. After rotating the structure so that the four atoms can be clearly seen, measure and display the numerical value of φ using the technique described above. <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_draw_rama/5'>Confirm</scene> the direction of rotation and the values of ψ and φ.

== Determine values of other ψ and φ angles ==

Ramachandran Plot: Difference between revisions

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Revision as of 03:47, 6 June 2010 view source Wayne Decatur (talk \| contribs) Editor, widgeteditor 7,824 edits m added simple solution of how to get model back after using command to get plot ← Older edit		Revision as of 17:01, 18 August 2010 view source Karl Oberholser (talk \| contribs) 1,665 edits →Torsional (dihedral) angles Newer edit →
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	<scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_planes/2'>Draw planes </scene> of two peptide bonds. The <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_halos_psi/6'>four atoms </scene>making up ψ remain translucent, and the remaining atoms become transparent. After rotating the structure so that ~~the four atoms~~ can be clearly ~~seen~~, determine and display the numerical value of ψ by double clicking on a nitrogen of the peptide bond, single clicking on the next two atoms and then double clicking on the second nitrogen. (If the structure rotates in the course of clicking on the atoms or if you encounter some other problem, re-click on the green link 'four atoms' and restart the clicking on the atoms.) The <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_halos_phi/5'>four atoms</scene> making up φ remain translucent, and the remaining atoms become transparent. After rotating the structure so that the four atoms can be clearly seen, measure and display the numerical value of φ using the technique described above. <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_draw_rama/5'>Confirm</scene> the direction of rotation and the values of ψ and φ.		<scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_planes/2'>Draw planes </scene> of two peptide bonds. The <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_halos_psi/6'>four atoms </scene>making up ψ remain translucent, and the remaining atoms become transparent. After rotating the structure so that you can clearly see that you are not clicking on a transparent atom, determine and display the numerical value of ψ by double clicking on a nitrogen of the peptide bond, single clicking on the next two atoms and then double clicking on the second nitrogen. (If the structure rotates in the course of clicking on the atoms or if you encounter some other problem, re-click on the green link 'four atoms' and restart the clicking on the atoms.) The <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_halos_phi/5'>four atoms</scene> making up φ remain translucent, and the remaining atoms become transparent. After rotating the structure so that the four atoms can be clearly seen, measure and display the numerical value of φ using the technique described above. <scene name='User:Karl_Oberholser/Ramachandran_Plots/First_view_draw_rama/5'>Confirm</scene> the direction of rotation and the values of ψ and φ.

	== Determine values of other ψ and φ angles ==		== Determine values of other ψ and φ angles ==