This workshop series has been completed. No further workshops will be offered in this series. The last meeting (third day for the 5th group) was June 22, 1999. Workshops initiated and funded by the host organization may still be arranged.

The approach used in these workshops has been superceded in late 1999 by the Protein Explorer and its built-in tutorial. Nevertheless, all training documents prepared for and tested in these workshops remain available for use in 3rd party workshops or individual study.

Free Molecular Visualization Workshops for Biological Science College Faculty

Supported by the National Science Foundation Division of Undergraduate Education (Undergraduate Faculty Enhancement), and the University of Massachusetts.

  • Goals
  • Who is Eligible?
  • Time Commitment
  • Agenda
  • Faculty/Facilities
  • Web Site
  • Costs
  • Dates
  • Registration
  • Information for Participants
  • Goals

    Understanding the three-dimensional structures of proteins, DNA, RNA, and their interactions is difficult from flat pictures, yet grasping structure is important to understanding function. These hands-on workshops prepare college faculty to incorporate molecular visualization into their biological sciences teaching. Molecular images can be used to illustrate lectures, in student computer laboratories, or for self-paced out-of-class assignments. Teachers of large freshman and sophomore classes from both 2- and 4-year colleges are especially encouraged to participate.
    Chemists may be interested in other NSF-supported workshops on modeling of small molecules held in western MA at UMass/Amherst and in southeastern PA at Lebanon Valley College in Annville, PA.

    Familiarity with basic computer use and web browsing would be helpful but is not necessary; no prior experience with molecular visualization is assumed. The software runs with either Windows or Macs. Each workshop participant will be provided a computer (Amherst: Windows or Mac as preferred; LIU: Windows).

    Who is Eligible?

    These workshops are for full-time U.S.A. college faculty (2-year or 4-year). Because of the requirement to travel to the workshop site at your own expense, participants will be drawn primarily from the New England states of the USA. Other teachers who apply (high school, Canadian, TA's, part-time) will be put on a waiting list and admitted on a space-available basis shortly before the workshop. Researchers who do not teach are not eligible. These priorities are set by the funding program. Note that the software and documentation needed to learn to use it are already available at the RasMol Classic Main Page.

    Time Commitment

    Training: Each participant will attend three one-day (9-5) sessions. None of these days are consecutive, so participants will need to travel to the workshop site on three separate occasions. The first two days will be separated by several weeks; the third day will be approximately one year later (see agenda below).

    Use: In the academic year intervening between the second and third sessions, each participant will be expected to use molecular visualization as a component of teaching one or more class meetings.

    Dissemination: Each participant will be asked to identify and mentor two faculty colleagues.

    Faculty & Facilities

    The workshops will be led by Eric Martz, a Professor in the Department of Microbiology (UMass, Amherst). Martz has innovated molecular structure tutorials which are in use throughout the USA and in dozens of other countries. The web site he created served two million files to 90,000 people from 90 countries during the past year. The Amherst MA workshops will be held in the spacious Chemistry Resource Center (CRC), equipped with networked Windows 95/NT4 and Mac PPC (7100/80) stations (Dr. Beatrice Botch, Director). The CRC is supported by grants from the NSF and the Howard Hughes Medical Institute. The Long Island U/Brooklyn workshops will be held in a computer lab equipped with Windows 95 PC's.


    Antibody molecule (Immunoglobulin G)

    Day 1: Exploring the RasMol Classic Main Page with Netscape. Downloading and installing RasMol and Chime from the web. Using RasMol to visualize protein and DNA structure. Finding and downloading atomic coordinate files for molecules of your choice from the Brookhaven Protein Data Bank (PDB) via the web. Viewing animated tutorials in Chime. Introduction to scripting prepared views.

    Interval 1 (about 2 weeks, at home): Install RasMol and Chime on your computer. Help your mentorees with installation and introduce them to the software. Download and explore molecules of your choice. Plan uses of RasMol and/or Chime in your classes.

    Day 2: With the molecule(s) of your choice, you will use RasMol to save scripts, and then install these in a Chime template for a web-based teaching presentation.

    Interval 2 (about one year): Complete plans and implementation and incorporate molecular visualization into your classes. Continue training mentorees.

    Day 3: Each participant will report on their teaching experiences, what worked and what didn't work. Through discussion, the group will arrive at strategies which are effective in a variety of teaching contexts. Some time will be reserved for hands-on experience with molecular visualization freeware/upgrades which became available during the past year.

    Web Site

    Adenosine:Thymidine base pair from a
    Chime-based tutorial on DNA
    You can get a more concrete impression of what this workshop is about by visiting the
    RasMol Classic Main Page ( There you will find a molecular image gallery, animated tutorials on protein and DNA structure, and help for beginners (or advanced users). This site served two million files to 90,000 people from 90 countries during the past year.

    Costs & Locations

    Participants will be responsible for their own travel and subsistence costs for the three separate days explained above, except as noted below. Therefore it is expected that most participants will be drawn from the Northeastern USA. There is no registration fee. All required software is free (RasMol, atomic coordinate/PDB files for specific molecules, MDL's Chemscape Chime, Netscape Navigator [free for academic use]). For each workshop day, lunch will be provided at no cost to participants.

    Amherst MA. Participants whose travel time exceeds two hours (80 miles, e.g. Boston) will be eligible for free overnight accommodations for the single night prior to each workshop; if your travel time exceeds five hours (~250 miles), you will also be eligible for free accommodations the night after each workshop. In calculating travel time, include 20-30 min after arrival in Amherst to find the parking garage and walk to the computer lab. The number of participants for whom accommodations can be provided is limited by budget; accommodations will be allocated first-come first-serve, and will be double-occupancy.

    Long Island U/Brooklyn. These workshops are targeted to participants residing in the NYC metropolitan area. No overnight accomodations will be provided for participants at this site.

    Times & Dates

    All workshops will meet from 9:00 AM to 5:00 PM. It is recommended that you register for three dates which are all part of the same workshop group, such as all C, or all D. However, if you have scheduling conflicts, it is permissible to register for dates from different groups.

    Each participant comes for three separate days. All participants in a group (about 20 people) come on the same first and last days. The middle day is for individual projects, so the group is divided into two subgroups (e.g. group C is divided into subgroups C1 and C2, about 10 people each). Thus within each group schedule, you have a choice of either of two dates for the middle day.

    Five workshops, A through E (20 participants per workshop), are completed or in progress. Their locations and dates are available on the Ongoing and Past Workshops Page.

    The earliest date for a new workshop will be in spring 1999, and locations and dates have not yet been set. These will be available here as soon as they have been set. Meanwhile, if you are interested in participating, contact Eric Martz so you can be notified by email when the locations and dates are set.


    You can print a registration form here and now for Amherst MA or Long Island U/Brooklyn NY , or request a form by email from (BE SURE YOU HAVE SET YOUR RETURN ADDRESS IN NETSCAPE'S OPTIONS, MAIL PREFERENCES, IDENTITY BEFORE CLICKING HERE) or FAX a request to 413-545-2532. Register early to reserve a place.

    Last updated October 29, 1997.
    A one-page announcement designed to be printed is also available.
    Feedback to Eric Martz.

    Thanks to Rashie Athukorala for help in workshop preparations, and to Manik Ahuja and Chris Finlayson for help in getting the word out to faculty throughout New England.