Updated July 14, 2022.
(Submit these files through Canvas.) Professor McCallum should be able to open all necessary files submitted. A good submission should include a VMD Saved State. Be careful! You need to include the PDB file along with the saved state file! In addition, some sort of text file (Word processor file if that's all you can do) is included to describe your answers. For example for Assignment 1, you might submit:
- 1anv.pdb
- Part1.vmd (saved state file using 1anv)
- Part1.jpg
- Using the 103d molecule, create a JPG of a view looking down the helix (from the "top"), with a high-resolution ball-and-stick drawing method, and the atoms colored by type (standard colors). Save the state ("visualization state") of your view, as well as an image. In order to save an image, you may take a simple screen shot, or use the "File -> Render" menu. The default is ".tga", but you can change the suffix to ".png" or ".jpg".
- Using the solvated micelle PDB file, create a separate selection for each component (dodecyl sulfate, sodium ions, and water). Try and create a graphical representation which shows all three components in a clear way. You will most likely need to use a different representation for each specie. Again, once you are satisfied, save the VMD state to a file, and render an image to JPG. Determine the size (diameter) of the micelle using appropriate tools, and compare this to both the size (length) of a amphiphile, and the size of a water molecule.
- Using the solvated micelle system, determine how many water molecules are within 2, 5, and 10 angstroms of the micelle SURFACE. You will need to figure out somewhat advanced VMD selection syntax for this. As a hint, use the "Selections" tab under the "Graphical Representations" menu to help you find valid selections. (VMD allows all kinds of shorthand keywords such as "water", "helix", "peptide". It also allows negation—"not water"— and joining—"not water and peptide". As an example, "not water" might include a protein and any ions.)