Update for Participants in the
NSF Workshops on Molecular Visualization in Biological Science Teaching
Eric Martz, August 2000
This document is on-line at
Original workshop documents: www.umass.edu/microbio/rasmol/ws_docs.htm
The workshops you attended focused on two major skills:
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Protein Explorer has completely superceded RasMol.
- How to use RasMol to explore macromolecules of interest to you.
- How to create web-delivered presentations using Chime.
Regarding item #2: The technology for creating presentations has not
been significantly improved since the workshops.
Protein Explorer version 1.5:
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:
- Protein Explorer is free and works on both Windows and Macintosh.
- The first view of each molecule is maximally informative, described
and interpreted by the FirstView page. Extensive help is available
- QuickViews provides simple,
logically organized yet powerful menus. Context-sensitive help
is automatically displayed, including color keys.
No RasMol commands needed!
- Although you don't need to use RasMol commands, it
understands all RasMol commands. Therefore experienced
RasMol users can adapt easily.
- Class websites can include molecule-specific
hyperlinks to Protein Explorer which
prespecify molecule(s) featured in the class.
lysozyme (PDB ID code 1hel) can be explored with a hyperlink to
- Protein Explorer is adopted by the Protein Data Bank as a 3D
structure viewer (but currently still offers version 1.0 -- see note
- FirstView and QuickViews described above.
- Seq3D displays the amino acid
sequence -- clicking on a residue or range identifies it in the 3D
- Contact surfaces (produced with one click!) give an uncluttered
overview of noncovalent bonds between two moieties, such as ligand
and protein, or DNA and protein.
- MSA3D colors a protein to reflect conservation and mutation,
based on a multiple protein sequence alignment. A complete tutorial
is provided, including instructions on how to use Biology Workbench
to construct a multiple protein sequence alignment.
- Cation-pi interactions can be displayed between lys or arg
sidechains and the faces of pi orbitals of aromatic rings (phe, tyr, trp)
which have partial negative charge.
- Salt bridges can be displayed.
- When a multiple-model ensemble (NMR file) is loaded, you are
informed automatically, and offered special buttons for model selection.
Other important new resources include:
World Index of BioMolecular Resources in Chime.
Newly a "Visitor-Maintained Index": additions or changes supplied
by visitors via web form are immediately alphabetized into the
subject and author indices. Visitors can enter hyperlinks,
describe the resource, and provide subject or molecule name
Two categories: Ready-To-Use Resources, and How To
Create New Resources. Version two, now in preparation, when
released will allow visitors to rate and comment upon indexed
resources. Visitor-Maintained Index program authored by Trevor
Kramer and Eric Martz.
Biochemistry in 3D.
A new, superb, state of the art Chime website with interactive tutorials
on protein architecture (from amino acids through peptides, secondary, tertiary
and quaternary structure), trimeric G proteins, bacteriorhodopsin, myoglobin
and hemoglobin. Written by Tim Driscoll, Freida Reichsmann and others.
Additional tutorials on protein structure, DNA and DNA-binding
proteins authored by Frieda Reichsman are at the second site below.
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.
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.
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.