Assignments for First Interval

for participants in the
NSF Workshops on Visualization of Biomolecules in Teaching
UMass, Amherst, Eric Martz PD

(If you are reading a paper version of this document, it is also available at

Please do the following in the two to three week interval between the first and second workshop sessions.

  1. For Your Teaching
    1. Install RasMol and Chime on your computer(s).
    2. List some molecules you would like to visualize in your class(es).
    3. Search the Brookhaven PDB for suitable atomic coordinate files and download them. (Structures have not been determined for many molecules!)
    4. With RasMol, explore the structures in these PDB files.
    5. Select structural features and views to show your class which can be effectively visualized with the available PDB's.

    6. Search for animated tutorials which may already be available on the web for molecules on your list.
      1. Check the Animated Tutorials web page at
      2. Try general web search engines, a list of which is available at

    7. Decide which pedagogic approach(es) you wish to try in your classes with the PDB's and other animated visualization resources you have found. See the separate document on pedagogic approaches at

    8. Gather the following to bring with you to the second workshop meeting:
      1. On diskettes, the PDB files you have downloaded for your molecules. (If they are large, and you know how, consider compressing them with WinZip or Stuffit Lite).
      2. URL's for relevant web resources you have found, including already-implemented animated tutorials if any.
      3. A plan specifying the molecules, structural features, views, and pedagogic approaches you wish to use in your classes. At the beginning of the second workshop meeting, you will be asked to share which class, which molecule(s) and what general pedagogic approach you have in mind.
      4. Questions which came up as you worked.

    The majority of the second workshop meeting will be devoted to implementing your plan. Hopefully you will have completed steps 1-4, and spent some time on steps 5-7 before the second meeting. If you have not finished steps 5-7, you can continue work on them during the second meeting. You can work at your own pace with expert help and advice available as needed. (There will be only 10 participants at each second workshop meeting.) Some group discussion time will be devoted to issues of pedagogy and examples.

    The goal of the second meeting is to get far enough with implementing a teaching plan that you can complete it on your own and use it during the coming academic year.

  2. For Your Mentorees
  3. Help your mentorees with as many of the steps above as you can get to. It is important to get them started now so they can plan visualizations for their fall courses. You can continue to help them with remaining steps after the second workshop meeting. (At the second workshop meeting, you will be asked how far you got with your mentorees during the first interval.)

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