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

University of Massachusetts, Amherst MA, June 1998
Eric Martz, emartz@microbio.umass.edu. Project Director
Chemistry Resource Center (CRC) Computer Lab, Goessman 152, Dr. Beatrice Botch, Director.
Assisted by Rashie Athukorala, Honor Glenn, Tim Driscoll, and Ken Rotondi.
Computer configuration by Frank Stolle.
Supported by the Undergraduate Faculty Enhancement Program of the Division of Undergraduate Education, NSF, and the University of Massachusetts.

If you are reading a paper version of this document, it is also available at http://www.umass.edu/microbio/rasmol/w1agend3.htm

Overview of Three Meetings and Two Intervals

Day 1: Installation and use of RasMol to visualize molecules of your choice.

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

Day 2: Development of RasMol scripts for your classes. Optionally put your scripts into a web-ready Chime presentation.

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

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


Overview of Day One

  1. Questionnaires. Netscape, RasMol Web Site, 9:00-9:30

  2. Intro to Participants and Workshop 9:30-10:10

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

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

  8. Chime, 3:30-4:00

  9. Demonstration of MAGE; STING 4:00-4:30

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

1. Questionnaires; Netscape, RasMol Web Site, 9:00-9:30

Goals: Macintosh Procedures: Windows Procedures:

2. Intro to Participants and Workshop, 9:30-10:10

Goals:

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

Goals: Windows:
Windows Working Folder = J:\MolVis
Macintosh:
Macintosh Working Folder = User's Folder:MolVis

 

Coffee Break! 10:30-10:45
 

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

Goals:
Mouse Click and Drag Summary
Action Windows Macintosh
Rotate X,Y Left button Unmodified
Translate X,Y Right button Command*
Rotate Z Shift-Right Shift-Command*
Zoom Shift-Left Shift
Slab Plane Control-Left** Control**
These mouse click-and-drag operations work in RasMol and similarly (but with some different details) in Chime.

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

**Options, Slab mode must be turned on (checked) before the slab plane can be moved.

Important features to try out:


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

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

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

Goals: Procedures: Notes:

7. Writing scripts for RasMol, 2:15-3:15

Goals: Procedures: Notes:

 

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


8. Chime, 3:30-4:00

Goals: Procedures:
  • Macintosh Installation: Installation of Chime 1.0 on the Macintosh is tricky at one point, whereas installation in Windows is totally automatic. Notes:

    9. Demonstration of MAGE; STING, 4:00-4:30

    Goals: Notes:

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

    Checkout


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