Shari Dunham/Peptide1: Difference between revisions

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New page: ==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'>...
 
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== Representations==
== Representations==
<scene name='79/796888/Peptide-1-ball-and-stick/2'>Ball-and-stick</scene> is the same as the default representation above, but just an end-on orientation of the peptide.
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-backbone-b-and-s/2'>Protein backbone</scene> is another representation that is useful for viewing just the backbone atoms of peptides and proteins.
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>  


The <scene name='79/796888/Peptide-1-backbone-b-and-s/3'>spacefill</scene> representation more accurately represents the space occupied by the electron cloud of each of the atoms.  This representation only shows the spacefill of the heteroatoms of the protein backbone, and starts from an end-on orientation.
Ribbon representation:  <scene name='79/796888/Peptide-1-backbone-b-and-s/5'>with protein backbone only</scene>
 
A <scene name='79/796888/Peptide-1-backbone-b-and-s/5'>ribbon</scene> representation is a more simplified rendering that is often used to trace the backbone location in large protein structures.


== Displaying Hydrogen Bonds ==
== Displaying Hydrogen Bonds ==
Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules.
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.
Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:
 
== 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).
*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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