Sandbox 1742
From Proteopedia
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| - | ==Protein Secondary Structure Activity: | + | ==Protein Secondary Structure Activity: Peptide 1== |
<StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'> | <StructureSection load='Dunham-Peptide1.pdb' size='580' side='right' caption='Peptide 1' scene='79/796888/Peptide-1-ball-and-stick/1'> | ||
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== Representations== | == Representations== | ||
| - | <scene name='79/796888/Peptide-1-ball-and-stick/2'> | + | Ball and stick representations: <scene name='79/796888/Peptide-1-ball-and-stick/2'>with side chains</scene>, or <scene name='79/796888/Peptide-1-ball-and-stick/3'>with protein backbone only</scene> |
| - | <scene name='79/796888/Peptide-1- | + | Space fill representations: <scene name='79/796888/Peptide-1-ball-and-stick/4'>with side chains</scene>, or <scene name='79/796888/Peptide-1-ball-and-stick/5'>with protein backbone only</scene> |
| - | + | Ribbon representation: <scene name='79/796888/Peptide-1-backbone-b-and-s/5'>with protein backbone only</scene> | |
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== Displaying Hydrogen Bonds == | == Displaying Hydrogen Bonds == | ||
| - | + | Let's view the hydrogen bonds that can be calculated from optimal distances/angles in this structure: for the structure <scene name='79/796888/Peptide-1-ball-and-stick/7'>with side chains</scene>, or <scene name='79/796888/Peptide-1-ball-and-stick/8'>with protein backbone only</scene>. Use one of these representations to measure the distances necessary to complete the table in your activity. | |
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| - | == Measuring Distances Between Atoms == | + | == A Reminder on Measuring Distances Between Atoms == |
| - | + | *You might want to toggle off the spinning of the molecule (see spin button in lower left corner of the structure box). | |
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| - | *You might want to | + | |
*Put your cursor in the structure window. | *Put your cursor in the structure window. | ||
*Decide on two atoms for which you would like to measure the distance between them. | *Decide on two atoms for which you would like to measure the distance between them. | ||
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*Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units. | *Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units. | ||
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| - | == Measuring Angles formed by 3 Atoms == | ||
| - | To measure the angle formed by three atoms in the Model, you can follow steps very similar to those for measuring distances: | ||
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| - | *Stop the spinning of the Model. | ||
| - | *Hover your cursor over the first atom and double-click on that atom. | ||
| - | *Single-click on the second atom (the middle one). | ||
| - | *Finish by double-clicking on the third atom. An angle label should now appear on the structure. | ||
</StructureSection> | </StructureSection> | ||
Current revision
Protein Secondary Structure Activity: Peptide 1
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