Updated July 14, 2022.
Using VMD to clearly communicate information is the goal of this assignment. The more information your image(s) can say about the protein, the better. Be careful! MORE information does not necessarily mean more GRAPHICS! You may want to experiment with different background colors (but points will be taken off for yellow or green ;), transparencies, etc.
For example for Assignment 2a, you might submit:
- 1anv.pdb
- Part1.vmd (saved state file using 1anv)
- Part1.jpg
- Part1-zoomed.jpg (maybe a detail or zoom of your overall image).
For Assignment 2c, you might submit:
- The PDB file
- Part3.vmd (saved state file)
- Part3-rmsd.jpg (image)
- Part3.txt (discussion)
Refer to the rubric (on Canvas) for additional guidelines.
- At the Protein Data Bank, download a protein that has a ligand attached to a metal reaction center (a good starting point is searching "enzyme metal multiple" and further refining the results to oxidoreductases). Use VMD to represent any metal atoms and salt ions (typically sodium and/or chloride, but others are possible) in a Van der Waals representation, the protein itself with ribbons or a cartoon, and the area around the metal(s) as licorice. Make an image of your system.
- Find a protein at the Protein Data Bank that utilizes the beta column to represent some data, and explain what the authors used it for. You can either save the file and open it in a text editor on your computer, or use the PDB Viewing functions to look at the file. The top of a PDB file typically contains a lot of useful background information about the system studied.) Use a representation in VMD that expresses color according to the beta value (this is a selection choice in the "Coloring" choice in the Graphical Representations menu). It may be useful to read ahead a bit and look at the very first part of the PSF and PDB page.
- Finally, find a protein at the Protein Data Bank that consists of more than one structure (it may be 2, 5, 10 or more; 1SSE is an example of such a structure, and you may use this structure if you cannot find another example). These are usually obtained from NMR measurements. Load each structure into VMD and use the RMSD tool or Timeline tool to determine their relative RMSDs. Using appropriate representations, highlight which parts of the structures remain mostly static, and which parts are more fluid. You may use color, representations, color by RMSD, or any other VMD tool you think helps you explain. What conclusions can you make about the structure and function of the parts of the protein(s)?