Backbone representations: Difference between revisions
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==Ribbon Backbone Trace== | ==Ribbon Backbone Trace== | ||
Perhaps the most common backbone representation is the <scene name='59/599354/Helix/10'>ribbon</scene>. Here the <font style="color:#ff0080;"> ribbon is violet </font>, the [[DRuMS#Element|standard secondary structure color]] for alpha helices. As you can see, the ribbon is a smoothed backbone trace expanded in width. | Perhaps the most common backbone representation is the <scene name='59/599354/Helix/10'>ribbon</scene>. Here the <font style="color:#ff0080;"> ribbon is violet </font>, the [[DRuMS#Element|standard secondary structure color]] for alpha helices. As you can see, the ribbon is a smoothed backbone trace expanded in width. The''' arrowhead''' at one end points to the carboxyl terminus. | ||
*Here is the <scene name='59/599354/Helix/11'>ribbon alone</scene>. | *Here is the <scene name='59/599354/Helix/11'>ribbon alone</scene>. | ||
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==Protein Domain Example== | ==Protein Domain Example== | ||
Now lets look at a <scene name='59/599354/Domain/1'>small protein domain</scene> ([[1pgb]]). This domain contains the alpha helix used above, but also contains a small beta sheet made of four beta strands, plus loops (regions that are neither alpha helix nor beta strand) connecting the helices and strands. The helices and strands are represented as ribbons, while the "ropes" connecting them are smoothed backbone traces. | Now lets look at a <scene name='59/599354/Domain/1'>small protein domain</scene> ([[1pgb]]). This domain contains the alpha helix used above, but also contains a small beta sheet made of four beta strands, plus loops (regions that are neither alpha helix nor beta strand) connecting the helices and strands. The helices and strands are represented as ribbons, while the "ropes" connecting them are smoothed backbone traces. This type of representation is properly called a '''secondary structure schematic''', but is called a '''cartoon''' in [[Jmo]] and its family of visualization programs ([[RasMol]], [[Chime]]). '''Arrowheads''' point towards the carboxy terminus. | ||
*Lets <scene name='59/599354/Domain/2'>color by secondary structure</scene>: | *Lets <scene name='59/599354/Domain/2'>color by secondary structure</scene>: | ||
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{{Template:ColorKey_Loop}}. | {{Template:ColorKey_Loop}}. | ||
<scene name='59/599354/Domain/3'>domain | *For comparison, here are <scene name='59/599354/Domain/3'>all the atoms in this domain</scene>. | ||
<scene name='59/599354/Domain/4'> | *Here are the <scene name='59/599354/Domain/4'>atoms alone</scene>, without the ribbon. | ||
<scene name='59/599354/Domain/5'>backbone</scene> | *A simple <scene name='59/599354/Domain/5'>backbone</scene> for this small domain. | ||
<scene name='59/599354/Domain/6'>backbone | *The domain <scene name='59/599354/Domain/6'>backbone plus the smoothed backbone trace</scene>. | ||
<scene name='59/599354/Domain/7'>trace</scene> | *The <scene name='59/599354/Domain/7'>smoothed backbone trace alone</scene>. | ||
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
<references/> | <references/> | ||
