Workshop on Molecular Visualization for Biological Science Teaching: RasMol and Chime -- 3rd Meeting, April 1999

Long Island University, Brooklyn NY
Eric Martz, emartz@microbio.umass.edu. Project Director
Library Learning Center Room LLC 234B, Delicia Garnes, Director.
LIU Liason, Professor Anthony DePass.
Assisted by Srinivas Turaga
Computer configuration by Ralph Dorsinville.
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/w3agend2.htm

9:00-9:30 Fill out progress report; Copy your scripts or Chime presentation for projection.
9:30-Noon Share teaching experiences and resources created for teaching. Discuss pedagogy.
12:00 NOON - 1:00 PM (-: (-: (-: (-: Lunch! For Goodness Steak :-) :-) :-) :-)
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:
  - Friday: My Computer, C:\Friday
  - Saturday: My Computer, C:\Saturday
- Handouts improved or created since you attended the workshop a year ago are available under Information for Participants at the web site for these Workshops.
Optional work with new or upgraded software:
- PDB Lite
- Protein Explorer
- Amino Acid Quizzer
- World Index of Animated Tutorials in Chime and its associated Guestbook
- Chime 2, where you should see the Demonstrations. Be sure to try the Select Menu (click on MDL for the menu). Here are some contact surfaces for retinoic acid binding protein, SH3 domain of Grb3 binding a peptoid, or antibody Fv binding a peptide fragment of lysozyme antigen.
- What's New 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.
- Noncovalent Bond Finder
- Protein Morpher
- IR Spectra in Chime 2 mapped to animations of bond vibrations, at Paul Lahti's site (Mass) or Robert Lancashire's in Jamaica: p-xylene or acetophenone.
4:30-5:00 PM -- Before departing please: Write evaluation of today (blue paper)