Workshop on Molecular Visualization for Biological Science Teaching: RasMol and Chime

Eric Martz, emartz@microbio.umass.edu. Dept. Microbiology, U. Mass., Amherst MA.
Chemistry Resource Center (CRC), Goessman 152, Dr. Beatrice Botch, Director.
Assisted by Rashie Athukorala, Honor Glenn, and Tim Driscoll.
Computer configuration by Frank Stolle.
Supported by the Undergraduate Faculty Enhancement Program of the Division of Undergraduate Education, NSF, and the University of Massachusetts. Summer, 1997.

If you are reading a paper version of this document, it is also available at http://www.umass.edu/microbio/rasmol/w1agenda.htm

Overview of Three Meetings and Two Intervals

Day 1: Installation and use of RasMol and Chime for molecules of your choice.

Interval One: (2-3 weeks) Install software, locate PDB files, develop teaching plan. Help mentorees.

Day 2: Pedagogy. Implementation of teaching plan with technical help.

Interval Two: (1 year) Complete implementation, incorporate into teaching, assess.

Day 3: Report accomplishments and assessments to group. Recommend and discuss improvements in pedagogy. Software update.


Overview of Day One

  1. Questionnaires, Intro to Participants and Workshop 9:00-9:40

  2. Netscape, RasMol Classic Main Page, 9:40-10:10

  3. Downloading and Installing RasMol, 10:10-10:30

    * * * Coffee Break, 10:30-10:45 * * *

  4. Basic RasMol: mouse, pull-down menus, 10:45-11:15

  5. RasMol Commands, 11:15-12:00

    * * * Lunch! (Campus Center Room 1101), 12:00-1:30 * * *

  6. Downloading molecules of your choice from Brookhaven's PDB, 1:30-2:15

  7. Chime, 2:15-2:45

  8. Writing scripts for RasMol, 2:45-3:15

    * * * Coffee/Juice Break! 3:15-3:30 * * *

  9. Demonstration of MAGE, UCB-RasMol, 3:30-4:00

  10. Downloading, installing, running a RasMol "movie" script, 4:00-4:30

  11. Assignments for Interval 1, Discussion 4:30-5:00

1. Questionnaires, Intro to Participants and Workshop, 9:00-9:40

(See separate list of participants with email addresses.)

2. Netscape, RasMol Classic Main Page, 9:40-10:10

Goals: Mac Procedures: Windows Procedures:

3. Downloading and Installing RasMol, 10:10-10:30

Goals: Macintosh: Windows:

4. Basic RasMol: mouse, pull-down menus, 10:45-11:15

Goals:
Action Macintosh Windows
Rotate X,Y Unmodified Left
Translate X,Y Command* Right
Rotate Z Shift-Command* Shift-Right
Zoom Shift Shift-Left
Slab Plane Control Control-Left
These mouse click and drag operations work in RasMol and also in Chime.

*Command is the "Apple" key. In RasMac the Option/Alt key seems to work interchangably with the Command key.

Important features to try out:


5. RasMol Commands, 11:15-12:00

Goals: Notes:
Lunch! (Campus Center Room 1101), 12:00-1:30

6. Downloading molecules of your choice from Brookhaven's PDB, 1:30-2:15

Goals: Procedures: Notes:

7. Chime, 2:15-2:45

Goals: Procedures: Notes:

8. Writing scripts for RasMol, 2:45-3:15

Goals: Procedures: Notes:

 

Coffee/Juice/Cookie Break! 3:15-3:30
 

9. Demonstration of MAGE, UCB-RasMol, 3:30-4:00

Goals: Notes:

10. Downloading, installing, running a RasMol "movie" script, 4:00-4:30

Goals: Procedures: Notes:

11. Assignments for Interval 1, Evaluation, Discussion, 4:30-5:00

Checkout


Thanks to Rashie Athukorala for assistance with parts of this document.