User:Eleanor Crabb/Sandbox 1
From Proteopedia
(Difference between revisions)
| Line 2: | Line 2: | ||
The interactive image on the right shows the protein with the pdb code 1z3a. You can rotate the molecule using your mouse and zoom by holding down the shift key while you move the mouse. | The interactive image on the right shows the protein with the pdb code 1z3a. You can rotate the molecule using your mouse and zoom by holding down the shift key while you move the mouse. | ||
| - | You will note that | + | You will note that there are two chains in this protein,shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green. |
This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note that the H atoms are not shown): | This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note that the H atoms are not shown): | ||
| Line 8: | Line 8: | ||
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/1'>space- filled</scene> - this gives an indication of the size and shape of the protein | *<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/1'>space- filled</scene> - this gives an indication of the size and shape of the protein | ||
*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene> | *<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene> | ||
| - | Let us now look at just a single length of the chain. | ||
| - | <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ball/1'>chain A ball and stick</scene> | ||
| + | Let us simplify things further by looking at just a | ||
| + | <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ball/1'>small portion </scene> of the chain. If we now draw a line through the backbone of the chain illustrated as <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ballcartoon/1'>the cartoon with the residues</scene> or the | ||
| + | <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone. | ||
| + | Returning now to <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>Chain A</scene>. This can be coloured according to: | ||
| + | *the arrangement of the residues is the primary structure coloured according to <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_res/1'>residue</scene>. | ||
| - | + | *<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_nc/1'>NC</scene> | |
| - | + | *<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_2nd/1'>Secondary structure</scene> | |
| - | + | ||
| - | <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_nc/1'>NC</scene> | + | |
| - | + | ||
<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_active_site/1'>residues within 30 nm</scene> | <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_active_site/1'>residues within 30 nm</scene> | ||
Revision as of 21:54, 18 September 2009
|
The interactive image on the right shows the protein with the pdb code 1z3a. You can rotate the molecule using your mouse and zoom by holding down the shift key while you move the mouse.
You will note that there are two chains in this protein,shown in green and blue. For simplicity let us concentrate on just a , chain A. To see this click on the link in green.
This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note that the H atoms are not shown):
- - this gives an indication of the size and shape of the protein
Let us simplify things further by looking at just a of the chain. If we now draw a line through the backbone of the chain illustrated as or the alone.
Returning now to . This can be coloured according to:
- the arrangement of the residues is the primary structure coloured according to .
