Update for Participants in the NSF Workshops on Molecular Visualization in Biological Science Teaching
Eric Martz, August 2000
This document is on-line at www.umass.edu/microbio/rasmol/wsupdate.htm
Original workshop documents: www.umass.edu/microbio/rasmol/ws_docs.htm

The workshops you attended focused on two major skills:

  1. How to use RasMol to explore macromolecules of interest to you.
  2. How to create web-delivered presentations using Chime.
Regarding item #1: Exploration of macromolecules has become much easier with the release of Protein Explorer version 1.5 in July, 2000. You no longer need to remember, look up, or type any RasMol commands! And Protein Explorer is more powerful than RasMol, enabling you to create exciting new kinds of molecular visualizations (see below). For exploring macromolecular structure, Protein Explorer has completely superceded RasMol.

Regarding item #2: The technology for creating presentations has not been significantly improved since the workshops.


Protein Explorer version 1.5:
www.umass.edu/microbio/chime/explorer
Note that the Protein Data Bank is not yet offering version 1.5. After you find a molecule at the Protein Data Bank, note the 4-character PDB ID code, then go to the above URL to explore it in version 1.5.
Protein Explorer includes these powerful features not available in RasMol:


Other important new resources include:


The following important resources are being maintained. They will be new to those of you who took the earlier workshops, but were introduced to those taking the later workshops.

  • PDB Lite. A search interface for the Protein Data Bank designed for students, educators, and occasional users. Jargon is avoided or explained. Detailed instructions for downloading PDB files so you can open them in RasMol or Protein Explorer, Tabular summary is easy to scan. Disallows syntax which gives false misses. Automatic synonym searching ("hemoglobin" finds "haemoglobin"). Mirrored around the globe. Authored by Eric Martz and Jaime Prilusky.
    www.umass.edu/microbio/rasmol/pdblite.htm

  • NonCovalent Bond Finder. An automated tool in Chime that finds the closest contacts between any two sets of atoms. Pressing the [Find] button repeatedly steps out in 0.1 Angstrom increments. Fill out the residues to which atoms belong in a single click. By Eric Martz, released in 1998.
    www.umass.edu/microbio/chime/find-ncb