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/> | ||
Revision as of 21:54, 19 September 2014
THIS ARTICLE IS UNDER DEVELOPMENT AND IS CURRENTLY INCOMPLETE. Eric Martz 20:18, 19 September 2014 (IDT)
Backbone representations are simplified 3D depictions of proteins or nucleic acids that enable the polymer chain structure to be seen. In proteins, a simple backbone trace connects alpha carbons (balls) but the backbone trace line does not coincide with any of the covalent bonds in the main chain ().
Protein Main ChainLets begin with (15 amino acids)[1] The atoms and bonds are colored by element: C H O N.
Protein Backbone Trace: Now we'll draw a yellow line between alpha carbons (balls). This line is called a backbone trace .
Smoothed Protein Backbone TraceA is another common backbone representation. Here, the smoothed backbone trace is green .
Ribbon Backbone TracePerhaps the most common backbone representation is the . Here the ribbon is violet , the 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.
Protein Domain ExampleNow lets look at a (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.
Alpha Helices, Beta Strands , Loops .
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