User:J. Shaun Lott/BIOSCI 203: Difference between revisions

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<scene name='User:J._Shaun_Lott/BIOSCI_203/All_atoms_view/1'>here</scene> for an 'all atoms' view of the protein. This will show us all the atoms (except for the hydrogens) coloured by the 'CPK' colour scheme we talked about in lectures - blue for nitrogen atoms, red for oxygen atoms, grey for carbon atoms and yellow for sulfur atoms. Pretty hard to see what's going on, isn't it?

We can simplify things by just showing a cartoon that traces the path of the amino acid backbone; α-helices are shown as coils, and β-strands as arrows pointing in the direction of the C-terminus of the protein. <scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_rainbow/2'>Here</scene> is a version with the cartoon coloured from blue at the N-terminus to red at the C-terminus. <scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_elements/1'>Here </scene>is a version with the β-strands coloured yellow and the α-helices coloured pink.

We can simplify things by just showing a cartoon that traces the path of the amino acid backbone; α-helices are shown as coils, and β-strands as arrows pointing in the direction of the C-terminus of the protein. <scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_rainbow/3'>Here</scene> is a version with the cartoon coloured from blue at the N-terminus to red at the C-terminus. <scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_elements/2'>Here </scene>is a version with the β-strands coloured yellow and the α-helices coloured pink.

It can help to see the

<scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_hbonds/2'>backbone hydrogen bonds</scene> that define the secondary structure elements, and sometimes this is clearer shown as a <scene name='User:J._Shaun_Lott/BIOSCI_203/Backbone_hbonds/1'>backbone trace</scene> which just shows links between the Cα atoms, rather than a ribbon diagram.

<scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_hbonds/3'>backbone hydrogen bonds</scene> that define the secondary structure elements, and sometimes this is clearer shown as a <scene name='User:J._Shaun_Lott/BIOSCI_203/Backbone_hbonds/1'>backbone trace</scene> which just shows links between the Cα atoms, rather than a ribbon diagram.

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 <scene name='User:J._Shaun_Lott/BIOSCI_203/All_atoms_view/1'>here</scene> for an 'all atoms' view of the protein. This will show us all the atoms (except for the hydrogens) coloured by the 'CPK' colour scheme we talked about in lectures - blue for nitrogen atoms, red for oxygen atoms, grey for carbon atoms and yellow for sulfur atoms. Pretty hard to see what's going on, isn't it?
-We can simplify things by just showing a cartoon that traces the path of the amino acid backbone; α-helices are shown as coils, and β-strands as arrows pointing in the direction of the C-terminus of the protein. <scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_rainbow/2'>Here</scene> is a version with the cartoon coloured from blue at the N-terminus to red at the C-terminus. <scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_elements/1'>Here </scene>is a version with the β-strands coloured yellow and the α-helices coloured pink.
+We can simplify things by just showing a cartoon that traces the path of the amino acid backbone; α-helices are shown as coils, and β-strands as arrows pointing in the direction of the C-terminus of the protein. <scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_rainbow/3'>Here</scene> is a version with the cartoon coloured from blue at the N-terminus to red at the C-terminus. <scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_elements/2'>Here </scene>is a version with the β-strands coloured yellow and the α-helices coloured pink.
 It can help to see the
-<scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_hbonds/2'>backbone hydrogen bonds</scene> that define the secondary structure elements, and sometimes this is clearer shown as a  <scene name='User:J._Shaun_Lott/BIOSCI_203/Backbone_hbonds/1'>backbone trace</scene> which just shows links between the Cα atoms, rather than a ribbon diagram.
+<scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_hbonds/3'>backbone hydrogen bonds</scene> that define the secondary structure elements, and sometimes this is clearer shown as a  <scene name='User:J._Shaun_Lott/BIOSCI_203/Backbone_hbonds/1'>backbone trace</scene> which just shows links between the Cα atoms, rather than a ribbon diagram.
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