Workshop on Molecular Visualization for Biological Science Teaching: RasMol and Chime -- 3rd Meeting, June 1998

University of Massachusetts, Amherst MA
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.

This document is on the web with hyperlinks at www.umass.edu/microbio/rasmol/w3agenda.htm

9:00-9:30 Fill out progress report; Login; Copy your scripts or Chime presentation for projection.
Methods Macintosh Login:
- Open the Apple menu, select Server Login.
- Enter your account, which is workshop## where ## is the two-digit number on your name tag. If your number is 07, your account is workshop07.
- Enter the password bondatom.
Macintosh Projection:
- Open "Macintosh HD", then "User's Files". Here, create a new folder named with your surname. Into the new folder, copy the files you wish to project. Verify that the files work in RasMol or Navigator. Ask for help if there are problems.
- Open "CRC Shared: users: temp:". Drag the folder with your surname, containing the files to be projected, dropping it into "temp" (which will copy, not move, the folder with its files).
- Inform Eric that your files are available to be projected.
Windows Login:
- Hold down Ctrl and Alt simultaneously while pressing Del to get the login window.
- Enter your username, which is workshop## where ## is the two-digit number on your name tag. If your number is 07, your username is workshop07.
- Enter the password bondatom.
- The domain must be CRC.
- Press the OK button.
Windows Projection:
- Copy the files to be projected into the folder J:\ToShow.
- Verify that the files work in RasMol or Navigator. Ask for help if there are problems.
- Inform Eric that your files are available to be projected.
9:30-Noon Share teaching experiences and resources created for teaching. Discuss pedagogy.
* * * Coffee Break, 10:30-10:45 * * *
12:00 NOON - 1:30 PM (-: (-: (-: (-: Lunch! :-) :-) :-) :-)
Blue Wall in the Campus Center -- Get a Ticket!
Demonstrations of new or upgraded software (see list below).

Individual Work -- Select What You Prefer
Optional review of how to use RasMol or build Chime presentations.
- A folder is provided on your computer containing RasMol, a variety of PDB files, and the current version of the Template for making Chime presentations with RasMol-saved scripts. This is your private working folder:
  - Macintosh: Macintosh HD: User's Files: MolVis3
  - Windows: My Computer, J:\MolVis3
- Handouts improved or created since you attended the workshop a year ago are available under Information for Participants a the web site for these Workshops.
* * * Coffee/Juice Break! 3:15-3:30 * * *
Optional work with new or upgraded software:
- New Chime Template for RasMol-Saved Scripts
- PDB Lite
- World Index of Animated Tutorials in Chime
- What's New at the RasMol Classic Main Page and at the UMass Chime Resources Site
- Sequence to structure mapping: STING
- How do you document that instructional materials you create and put on the web are worthy scholarship? See the Permission statement at Gale Rhodes' Home Page (Dept. Chemistry, U. Southern Maine) where you will find some excellent tutorials for RasMol, Swiss PDB Viewer, and MAGE.
- New Features in Chime 2 (Windows Only*)
- Noncovalent Bond Finder (Windows Only*)
- Chime Presentation Maker (Windows Only*) [not yet ready to use]
- Protein Morpher (Windows Only*)
- Protein Explorer (Windows Only*) [Sorry, not yet on the web]
- IR Spectra in Chime 2 mapped to animations of bond vibrations, for p-xylene or acetophenone. (Windows Only*)
* Until Chime 2 is released for Macintosh (it will not be developed for Windows 3.1).
4:30-5:00 PM -- Before departing please: Write evaluation of today (blue paper)