Below is a list of additions/changes to
this site since it was established
on November 7, 1996,
most recent first.
From 1996-2005, resources employing
MDL Chime plugin were the focus of this site.
In 2004, this site was renamed to MolviZ.Org.
Starting in 2005, we began to offer resources employing the
Jmol java applet.
Starting in 2013, we began to offer resources employing
JSmol (no Java).
(The RasMol Home Page was established in 1995, a year
earlier than this site.
In 2008, it was renamed the
RasMol Classic Site.)
2015 (dates are given year/month/day)
- Many links were discovered to be broken.
Hopefully they are all fixed now! Please report any problem to martz at microbio dot umass dot edu.
[The problem may have resulted from an interaction between
a change (December, 2014?) in the Sitemeter visitor counter (bottom of page) and the way some
links on the page were coded.]
2014 (dates are given year/month/day)
- The main page at MolviZ.Org has been thoroughly upgraded (the first
systematic upgrade since 2007!).
- The Top5 page has also been systematically upgraded.
- Links to the following were removed:
- Tutorials and resources utilizing JSmol were marked
were provided for enabling Java in order to use tutorials that still depend on the
unsigned Jmol applet
2013 (dates are given year/month/day)
- Biochemistry in 3D, a site with 9 excellent tutorials to
accompany Lehninger Principles of Biochemistry, is linked under
Other Jmol Resources.
2010 (dates are given year/month/day)
- Major Histocompabibility Complex tutorial has been released.
- Lac Repressor article in Proteopedia.Org (Jmol)
has been linked to the main page.
2008 (dates are given year/month/day)
Added tutorial on Antibody in Jmol, ported
earlier Chime version.
- Added Proteopedia.Org to the main page and to
- Linked JTAT to Top 5.
- Under Water in Jmol on the main page, added that
liquid water and ice can also be visualized in this updated resource.
2007 (dates are given year/month/day)
- 2007/8/28: Added Periodic Table of the Elements in Jmol by Angel
- 2007/8/4: Added a new page describing the
MolviZ Top 5, and linked it to
- 2007/7/24: Added Jmol-based simulation of 10 water molecules
condensing into a droplet. Thanks to Angel Herráez for porting
this from Chime to Jmol.
- 2007/7/21: Added descriptions and links to Polyview-3D and the
ConSurf Server, and Karl Oberholser's tutorial on collagen.
- 2007/7/19: Tutorials in Jmol offered at MolviZ.Org for
the first time. At this time, only three Martz-authored tutorials
have been ported to Jmol: DNA Structure, Hemoglobin, and Lipid
Bilayers and Channels. Thanks to Angel Herráez
and Frieda Reichsman
who did these ports! Previously, MolviZ.Org offered some tutorials
in Jmol via BioMolecular Explorer 3D, and also offered FirstGlance in Jmol.
To complete this update, several MolviZ.Org documents now note that
Chime is being phased out, and Firefox is recommended
Browsers page (which also now mentions use of
a virtual Windows machine for Chime on Intel Macs).
(The following files were updated: abtchime.htm, chimgeck.htm,
getchime.htm, neccsoft.htm, news.htm, newchime.htm, netscape.htm,
- 2007/6/27: Biochemical Journal publishes its first
paper with interactive 3D replica figures (in Jmol). Authored
by Frieda Reichsman, you can find this paper (requires a subscription)
See earlier instances below at 2007/3-5 and 2006/12/15.
- 2007/5/14: Protein Explorer 2.80 released with updates to the slides
About Protein Structure/Structural Bioinformatics, explicit support
for Intel Macs, refusal to run in Internet Explorer 7 (does not support
Chime), and improved troubleshooting for Firefox 2 on Windows. The
Atlas of Macromolecules was updated, and now offers display in
FirstGlance in Jmol or Protein Explorer for each and every
- 2007/3-5: Two more papers in ACS Chemical Biology
now have interactive 3D replica figures (in Jmol). Viewing these requires
a subscription. See related news item below at 2006/12/15.
- 2007/4/16: Our hemoglobin tutorial, available in Chime since 1997,
available in Jmol, thanks to Frieda Reichsman
(MoleculesInMotion.Com). Neither this nor the Jmolized-DNA
Structure tutorials are linked
to MolviZ.Org yet, but that is in the works.
- 2007/1: FirstGlance in Jmol released as a display option for
Server, which predicts antibody epitopes (including
discontinuous epitopes) on a 3D protein antigen, based on the
sequences of peptides that bind to the antibody.
BioMolecular Explorer 3D
(for high school teachers)
version 2 released.
This version eliminates the problematic Chime plugin. All molecules
are viewed in the Jmol applet (nothing to install, works on Windows,
Mac OSX/Safari, linux).
Included is the original DNA double helix tutorial, kindly ported from
Chime to Jmol by Angel Herráez
is the lead developer in this project.
- 2007/1-6: One-day, hands-on workshops on protein molecular visualization
and structural bioinformatics
were taught, for the first time eliminating
Chime-based resources. These utilized
FirstGlance in Jmol for visualization, including
visualization of evolutionary conservation at the
ConSurf Server and specific oligomers from
Probable Quaternary Structure,
Polyview-3D for publication quality figures
and animations for Powerpoint presentations. Four cycles were taught
at the University of Massachusetts, Amherst, Amherst College, University
of Massachusetts Medical School in Worcester, and Osaka University, Japan.
Each had about 25 participants.
Fliers and syllabi available at
2006 (dates are given year/month/day)
- 2006/12/15: The journal Chemical Biology (American Chemical
Society) debuts the first paper in more than a decade
in which protein structure figures
are available in interactive 3D replicas. Since they are in Jmol,
there is nothing to install, and they are immediately viewable
in Windows (Internet Explorer or Firefox), Mac OSX (Safari or Firefox),
or linux (Firefox).
This amazing breakthrough was
accomplished by Frieda Reichsman
(MoleculesInMotion.Com), thereby ending the hiatus of more
than a decade since Protein Science stopped providing interactive
3D molecular views as Kinemages
History). Because of its significance, the journal
has made this paper and the figures in Jmol available free to
non-subscribers -- see
- 2006/12/10: FirstGlance in Jmol
version 1.0 released with What is FirstGlance in Jmol and
instructions for putting static snapshots of molecular views into presentations.
- 2006/10: FirstGlance in Jmol released as a display option for the
ConSurf Server, which colors a 3D protein structure
by evolutionary conservation, automatically. ConSurf results can be downloaded
as PDB files, and later uploaded to FirstGlance in Jmol, which will automatically
show them with ConSurf colors, and with the ConSurf control panel.
Biomolecules in the computer: Jmol to the rescue
by Angel Herráez
appeared in Biochemistry and Molecular Biology Education.
(jmol.org) is rapidly superceding Chime
for many compelling reasons. Other Jmol literature is in the
- 2006/6/20: Protein Explorer 2.78 Beta released
support for ConSurf 3. A downloaded copy of this version of PE will
display ConSurf job results (saved as PDB files) in the same way
they are displayed at the ConSurf server (see 2006/6/18). Also many bugs
fixed, improvements in export of MolSlides to Jmol, improvements to
ConSurf 3 released with many improvements both in the routines
that calculate evolutionary conservation, and in the display of the
results in Protein Explorer (see 2006/6/20).
The results of a ConSurf job can now be
as a single PDB file.
New in ConSurf 3?.
- 2006/5/10: FirstGlance in Jmol
version 0.991 released. Contacts.., Find.., Reset,
Snapshot Gallery, salt bridges and cation-pi interactions,
sequence to coordinates (to locate gaps), improved visibility
of non-standard residues and anomalous atoms, specifications
for an interactive sequence listing, improved the help, fixed bugs.
- 2006/3/13: FirstGlance in Jmol
version 0.98 released. PDB files can be uploaded. Hide; new features
under More Views..
- 2006: The February issue of
Nature Structure and Molecular
Biology introduced links to FirstGlance in Jmol
for convenient visualization of newly reported structures.
- 2006/2/12: FirstGlance in Jmol
version 0.97 released. Shows ligands and disulfide bonds by default.
Better handling of non-standard residues. Click-to-identify, More Views,
Mirror Sites. Bugs fixed, documentation improved.
2005 (dates are given year/month/day)
- 2005/11/26: FirstGlance in Jmol
version 0.96 released. This new, simple interface enables easy
exploration of any PDB file. It works in all popular browsers in
Windows, OSX, and linux without installing anything (except
java). Designed for scientists taking a first look at new
structures reported in professional journals, it offers less help
for beginners, and is less powerful, than Protein Explorer.
- 2005/09/02: BioMolecular Explorer 3D (released December 2004)
available on CD
to facilitate use in classrooms with slow (or no) Internet
- 2005/07/24: Released
Protein Explorer 2.76 Alpha, with many improvements in
- 2005/06/12: Released
Protein Explorer 2.75 Alpha, which introduces
a new History mechanism with which you can step through your past
views within the session, applying any past view to PE.
This version includes numerous improvements to the PE Recorder,
and enhancements to support for PiPEs.
3D (released December 2004 for high school teachers/students) has
been upgraded to work in Netcape 7, Firefox and Mozilla (on Windows).
Detailed instructions for installation have been provided.
Thanks to Frieda S. Reichsman
for these improvements.
2005/06/10: MolviZ.Org home page
redesigned and several sub-pages revised by Frieda S. Reichsman.
Instructions were added for use of the Gecko browsers (Netscape 7.2,
Firefox & Mozilla) with Chime on the How to
Download and Install Chime page and on the Chime: Browsers, Platforms, Installation,
Troubleshooting page, which also received substantial revision.
A new page called About Chime now holds much of the information about Chime itself that was previously on the MolviZ.Org home page and elsewhere. How to Download and Install Netscape 4.8 was updated to include a direct link to the current product archive site at Netscape.com and a more current description of how to find the archive if the link dies. The Chime test page was revised and dependent files placed with it in a directory so that it is portable.
- 2005/02/20-21: Protein Explorer 2.72, 2.721 Alpha:
Presentations in Protein Explorer (PiPEs) can now use more than
one PDB file per control panel, and pop-up windows with additional
details for each molecular view.
and click on the magenta link
to the Alpha version.
- 2005/01/31: Protein Explorer 2.71 Alpha fixes a couple of serious
bugs in the PiPEs support, and improves some of the instructions for
and click on the magenta link
to the Alpha version.
- 2005/01/26: Protein Explorer 2.7 Alpha has three major enhancements:
an Undo button, a command script "PE Recorder", and support for Presentations
in Protein Explorer (PiPEs).
An example of PiPEs is included, along with a template and instructions
for building your own PiPEs. Molecular views saved with the PE Recorder
can be attached to buttons in PiPEs.
and click on the magenta link
to the Alpha version. Thanks to Tim Driscoll (www.molvisions.com)
who implemented the PE
Recorder as well as designing it, with input from Frieda Reichsman and Eric
- 2005/01/26: Protein Explorer 2.45 Beta works in Netscape 7.1 or later
(as well as 4.x), and current versions of Mozilla and Firefox, as well as
Internet Explorer. Get this version with dozens of other minor enhancements
Thanks to Enrique Castro of the Universidad de Las Palmas de Gran Canaria
for crucial insights on how to make these "Gecko" browsers compatible with PE.
2004 (dates are given year/month/day)
BioMolecular Explorer 3D is a collection of 3D-interactive, biologically
significant molecules relevant to a high school biology curriculum.
Detailed instructions are provided for teachers.
- 2004/12/19: Released animations of the rotation of the
flagellar hook, a molecular universal joint.
This resource is part of the
Atlas of Macromolecules
- 2004/11/01: Moved the former "RasMol email list" to a new home:
morph of the lac repressor bending DNA as it goes from nonspecific
to sequence-specific binding, involving some opening of the minor groove.
This morph is part of the
Atlas of Macromolecules
- 2004/09/29: Provided new domain name MolViz.Org
as an easy way to remember access to the main site.
- 2004/09/12: Released
simulation of 10 water molecules falling
into a droplet (as part of Protein Explorer's Atlas).
- 2004/09/10: Released Protein Explorer
2.411 Beta, to cope with
the pop-up blocker released in Windows XP SP2 in August.
- 2004/08/21: Released Protein Explorer
- 2004/08/15: Linked Max Perutz interview movies to
Crystallography History Page.
- 2004/06/15: Protein Explorer 2.4 Beta released.
Added flash demonstration movies "Getting Started in
Protein Explorer" by
Frieda Reichsman. Provided help for Mac OS X users.
- 2004/06/10: Protein Explorer 2.25 Alpha
Spanish completed by volunteer Gabriel Pons, University of Barcelona.
- 2004/05: At the World Index of Molecular Visualization Resources
(molvisindex.org), expanded the
biochemical tutorials category to include any technology with rotating/interactive
molecular images (not just MDL Chime). Also added a new category
on Physical Molecular Models and Molecular Sculpture.
- 2004/05/07: Protein Explorer 2.3 Alpha released.
Improved Chime and browser testing, including detection of software
that blocks opening of pop-up windows ("pop swatters").
Fixed many bugs and further updated/improved documentation.
- 2004/04/20: Protein Explorer 2.2 Alpha released.
Control of window size greatly improved. Clarified Features of the
Molecule control panel.
Removed some alerts/warnings to streamline operation.
Added information about protein structure, including an
overview of Global Protein Structure Issues. Many documents
updated. Provided .sit downloads for Mac users.
- 2004/03/21: Updated, expanded and reorganized
About Chime at the bottom
of the main page, the title of which was also
Updated What Is Chime? and
Chime: Browsers, Platforms, Installation, Troubleshooting.
Created two new documents:
How to Download & Install Free MDL Chime
Version History of MDL Chime.
Updated broken links to Spanish and Portuguese translations.
- 2004/02/28: Added photos of a
gorgeous physical model of a DNA double helix
under Sculpture at the
History of Visualization of Biological Macromolecules.
2003 (dates are given year/month/day)
Visiting and use statistics on this site have been updated for the first
time in many years.
- 2003/09: Protein Explorer receives a MERLOT Classics Award for
"exemplary on-line learning resources". The award states in part "The Protein
Explorer has revolutionized the teaching of biology at a molecular level."
- 2003/07/07: Protein Explorer 2.1 Alpha is now available. Click on the
red link to 2.1 Alpha at the top of the FrontDoor at
2.1 Alpha can be
downloaded from the "Download" link at its FrontDoor (not the Beta FrontDoor).
2.1 Alpha adds a new control panel, "Features" of the molecule noted in the
PDB file header by its authors, and better internal navigation with a new
"PE Site Map". Click on the red "2.1 Alpha" at the 2.1 Alpha FrontDoor for
- 2003/02/15: A new site was released on
Science Education, complete with movies.
2002 (dates are given year/month/day)
- 2002/09/15: Protein Explorer 1.982 Beta provided
compatibility with Chime 2.6 SP4.
- 2002/09/08: Protein Explorer 1.981 Beta (access via
fixes two serious bugs affecting Mac PPC's, improves control
of surface coloring, and adds a DNA mismatch repair enzyme
to the Atlas. See if you can find the mismatched bases
(3rd item under "Challenging").
- 2002/08/30: Protein Explorer 1.98 Beta released (access via
This release works in Internet Explorer (as well as
Netscape 4.79) and includes a
few minor enhancements and many improvements to documentation
as well as many bug fixes, and a better installation procedure for
downloaded copies. It is slated to become version 2.0 (no longer
beta) after a suitable beta-testing period.
- 2002/07/08: Protein Explorer 1.86 is now available
en español thanks to
translation by Gabriel Pons (U Barcelona) and distribution
by Angel Herráez (U Alcalá, Madrid).
- 2002/07: The ConSurf Server
has been upgraded with the Internet Explorer-compatible version of
- 2002/06/25: The tutorial on DNA Structure
has been enhanced to work in Internet Explorer, has new
content on codons, and many new links under "more information on DNA".
- 2002/06/22: The main Chime Resources page
is now decorated with eleven new images, many animated.
- 2002/06/21: The main Chime Resources page
and the document on browser compatibility with
Chime have been revised to reflect the newly implemented
compatibility of some sites with Windows Internet Explorer. Changes
were made in Protein Explorer 1.901
to make the Win-IE-compatible test version (1.923) more obvious to IE
users. (Some of these changes are seen only when you view these sites with the
IE browser.) A new page was added on
how to find Netscape Communicator
4.7x at netscape.com.
- 2002/06/20: Hit meters have been added to the main pages of
a number of sites. Scroll to the bottom of the main page
and look for a visitor count. Clicking on the visitor count
will report an analysis of the browsers and operating systems
of visitors, as well as visiting rates. Results revealed that
two-thirds of visitors to the main page of Protein Explorer
were coming to the slow UMass site, rather than the
fast San Diego mirror site. Therefore, the existence
of the latter was made more obvious.
Also, because I am taking far longer than I would like to finish
Protein Explorer version 2.0, I have made a fast mirror of the
Win-IE compatible version 1.923 at
- 2002/02/21,24: The test version of Protein Explorer that works in
both Windows Internet Explorer and Netscape has been upgraded. The Atlas
of Macromolecules has been greatly expanded, and is now illustrated
with a gallery of small still images of featured proteins.
Improvements were made in Seq3D and the Troubleshooting guide, and
a new color scheme for distinguishing chains has been added. Click
on PE's version number for details.
- 2002/02/21: A new Atlas of Macromolecules has been started. It is
linked to the FrontDoor of
Protein Explorer. It includes clickable links to display exemplary
proteins in Protein Explorer.
2001 (dates are given year/month/day)
- 2001/12/20: A new version of Protein Explorer is available that
works in Windows Internet Explorer in addition to Netscape
(version 1.91). This is a
nearly-completed, alpha-test version. When completed, it will
supercede the last Netscape-only version (1.901).
In addition to Win-IE compatibility, a number of other
improvements were made,
including the addition of a new page listing
publications about PE (click on PE's version number for details).
- 2001/11: The ConSurf Server
is available for testing. It "identifies functional regions in proteins
by surface-mapping of phylogenetic information", and employs
Protein Explorer 1.901 to display the results.
ConSurf's solution to coloring a protein according
to a multiple sequence alignment and phylogenetic tree is more sophisticated
than the MSA3D available within Protein Explorer, which it supercedes.
- 2001/10/10: Chime tutorials from the UMass site on DNA,
Hemoglobin, and Antibody
are now available
Deutsch, thanks to Franz Josef Scharfenberger, Richard-Wagner-Gymnasium, Bayreuth.
Thanks to Gonzalo Claros, U. Malaga, available en Español
Gal4 transcriptional regulatory tutorial
as well as the
Lipid Bilayer and Gramicidin Channel tutorial announced below on
August 4, 2001.
- 2001/09/16: Recent updates to the page on
History of Visualization of Biological Macromolecules
by myself and Eric Francoeur
include a historical anecdote on the importance of wire backbone
models made with Byron's Bender in the first recognition of the
immunoglobulin superfamily fold, a photo of a 1996 molecular
sculpture in the Smithsonian, on-line digitized excerpts from 16
mm movies of very early protein computer graphics taken in Cyrus
Levinthal's group at MIT in the mid 1960's, and a paragraph on
the $250,000 Evans & Sutherland computers used in the mid-1980's
for fitting models into electron density maps.
- 2001/08/05,25,31: New versions of Protein
Explorer were released on these dates in August.
New features include Lesson Plans and Assessment tools, FAQ, and
instructions for mutating a protein model.
What's New? for full details.
- 2001/08/04: Gonzalo Claros (University of Malaga) has translated
the tutorial on DNA structure into
- 2001/04/24: Version 1.86 of Protein Explorer has information on
probable quaternary structures, crystal contacts, and how to get fewer or
single chains. These are new links in the Molecule Information Window. QuickViews
has a new display mode: Vines (backbone stem with sidechain leaves).
A new Glossary, Index and Help document was started, but is only partially
completed in this release.
- 2001/04/01: Angel Herráez has ported Lipid Bilayers and
the Gramicidin Channel to Chime (from my 1997 RasMol "Movie" Script).
He also translated it into
- 2001/03/11-18: Version 1.85 of Protein Explorer has faster,
more easily customizable, and more stable animations of
conformational changes. Several new morph animations were
added as examples. The animations can be saved for
playing in Netscape or Internet Explorer outside of Protein
Explorer. A QuickTour and a Troubleshooting guide have been
- 2001/02/04: The antibody tutorial has been
- 2001/02/04: A new presentation on Retinoid X Receptor
by Tanapat Palaga. This is a "Presentation in Protein Explorer" (PIPE), and the
first one made public that illustrates the newer features of PIPE. PIPE is
still under development and not yet available for authoring tutorials.
Earlier presentations in PIPE cover the bacterial cell division protein
FtsZ, and the SV40 virus capsid.
- 2001/02/01: Protein Explorer is now linked as a viewer for morphs
created at the
Yale morph server of Gerstein & Krebs.
- 2001/01/25: Protein Explorer 1.0 at the Protein Data Bank was fixed
(i) to allow Chime 2.6; (ii) to disallow Netscape 6; and (iii) to provide
a fork allowing either version 1.0 or 2-beta to be invoked.
- 2000/12/29: Protein Explorer
has been upgraded to version 1.80, with several enhancements to
the QuickViews menus, and a very annoying bug fixed at last.
- 2000/12/11: The long-obsolete document on browser compatibility
has been updated, now renamed
Chime: Browsers, Platforms, Installation, Troubleshooting
. It suggests methods for running Protein Explorer and other
UMass Chime Resources on linux, SGI, and other platforms.
- 2000/12/02: Eleven new categories have been added to
the World Index
of Molecular Visualization Resources, formerly concerned largely
with biochemistry resources in Chime. Visitors can now submit
resources for indexing by subject, title, and author
that are not in Chime, that concern organic or inorganic chemistry,
or that are targeted to K12 audiences. There is a category for Deep View
(Swiss-PDBViewer) resources. Sources of PDB files, galleries, email
discussions, and non-English resources can be listed, as well as
free and commercial software for molecular visualization.
- 2000/11/14: Protein Explorer has been
upgraded to version 1.72 beta. There is a new automatic reminder to
turn off spinning of the molecules when it is not needed, to avoid
"freezing" the computer with molecules spinning unnecessarily in
background windows during concurrent sessions, along with other
- 2000/10/04: Protein Explorer has been
upgraded to version 1.71 beta. Revision of the tutorial has been completed,
with answers available to teachers on request.
QuickViews menus were expanded, and new
"QuickViews Plus" options make QuickViews more flexible and powerful.
The domain name proteinexplorer.org now takes you to Protein
- 2000/09/07: Protein Explorer has been
upgraded to version 1.485 beta. The tutorial has been partially revised,
study questions were added, the advanced form for recording observations
was expanded, and a number of new functions were added to the QuickViews
menus. Click on What's New for a detailed list.
- 2000/08/29: At Protein Explorer, a box
now pops up offering to explain the Protein Explorer MSA3D
image in NetWatch in the September 1 2000
issue of Science. It shows enolase colored from a multiple
protein sequence alignment to show conserved residues.
- 2000/08/28: In a major transition, the
main page of this site
changed its emphasis from RasMol to Protein Explorer and Chime-based
presentations. Documentation of the
ease of use and power of Protein Explorer
- 2000/08/26: A new presentation is available that shows
in protein backbones. The backbone is shrunk in a movie until
the knot is clearly visible.
- 2000/08/24: The page on History of Molecular
Visualization has been updated to include rapid prototyping models,
and other new images.
Protein Explorer was upgraded to version 1.48. New features include
displays of cation-pi interactions, and salt bridges, and coloring a
protein by mutation/conservation from a multiple protein sequence
alignment (MSA3D). Tutorials are provided for each new feature.
- 2000/06/26: The section listing the van der Waals radii used
by Chime and RasMol for spacefilling and dots has been revised and expanded in the
FAQ. It now includes the "united atom"
radii previously disclosed only in the email list discussion (and still
not mentioned under 'spacefill' in the reference manual).
- 2000/06/02: A new World Index
of BioMolecular Resources in Chime has been installed.
It is "visitor-maintained" which should help to keep it much more
up to date than the old one. Thanks to Trevor Kramer for
implementing the support programs.
- 2000/06/02: DRuMS,
a proposed set of standard color schemes for
macromolecular visualization, is now available.
Protein Explorer has been upgraded to a new version
for beta testing. This version is much more user-friendly,
and has clickable sequence-to-structure mapping. This version
is able to supercede RasMol (unless you use SGI or linux),
as it has all RasMol's functionality for Windows or Macintosh,
but is easier to use and more powerful
- 2000/03/25: Added links to the Kleywegt Biomolecular Morphing site
and the Vonrhein movie in
version 1.51 of the
- 2000/02/28: Instructions for installing UMass Chime resources
have been revised. They are more detailed and include specific
sections for Windows, Macintosh, and SGI/Irix. See them
at the DOWNLOAD site.
- 1999/11/??: Protein Explorer 1.0 made available at the
Protein Data Bank.
- 1999/10/06: Protein Explorer 1.0 made available at the
test site of the Protein Data Bank.
- 1999/09/20: The
Protein Explorer has been upgraded to version 1.0. A complete
tutorial with built-in movies is now included, along with many other
enhancements. See What's New at the main page.
- 1999/08/03: The
Protein Explorer has been upgraded to version 0.992. A molecule
can now be pre-specified in a link to the Protein Explorer so that
it loads that molecule automatically. (The specification is as a query
The default location for fetching PDB files is now an operational one
(Cambridge UK), no longer Brookhaven, and three other working and up to date
mirror sites are listed. The control panels for generating surfaces and
contact surfaces have been enhanced.
This version also does more thorough compatibility checking of the client's
operating platform and browser.
- 1999/07/04: The Protein Morpher has
been upgraded to version 1.5. It now works fully on Macintoshes,
is downloadable, and methods are described for making your own morphs.
- 1999/06/29: The Noncovalent Bond Finder
has been upgraded to version 1.5. This version works on Macintoshes, expands
command aliases, and can be downloaded for local installation.
- 1999/06/16: The Protein Explorer
is the major focus of my (Eric Martz's) present work.
Like RasMol, you can
load any molecule and type commands, but it is easier to use and
more powerful. If you have used RasMol, you'll find this easy.
The tutorial for beginners is not yet completed,
which will make it more difficult for those who have never used RasMol before.
Version 1 of the Protein Explorer is less than 10% of what I have
planned -- wish us luck with our next NSF grant!
- 1999/06/09: Due to frequent inquiries about Chime for linux,
I have added an entry on this to the
FAQ. All questions about
support for Chime, Chime's Y2K compliance, etc. should be directed
to MDLI at firstname.lastname@example.org.
Interpreted Infrared Spectra: when you click on a peak,
the corresponding molecular vibration is animated in Chime!
This amazing work was done by Eric Motyka, Paul Lahti,
and Robert Lancashire. It can be
- 1999/04/11: A simple
Amino Acid Quizzer has been provided.
- 1999/02/11: An explanation of
how to gzip PDB files has been added
FAQ. This is important for PDB files put on web servers for use
with Chime, since it reduces Internet transfer time about 3.5-fold!
- 1999/02/11: The FAQ document has been linked to the main Chime
page under About Chime, where I
have also added links to some of the excellent recently updated
resources on MDL's Chime support site.
- 1998/11/08: The Noncovalent Bond Finder
has been modified in an attempt to allow loading of PDB files
in Macintosh Chime 2.
- 1998/11/03: MDL Information Systems, Inc. released
Chime 2 for Windows 95/NT and Macintosh!
- 1998/10/27: Inspired by a
class I'm teaching in macromolecular visualization, I've posted
a set of
design guidelines for chemical structure presentations in Chime,
which are linked under
Presenting RasMol-Saved Scripts with Chime.
- 1998/07/23: See java interacting with Chime via LiveConnect
in some amazing new ways: go to the links at the bottom of
the main page.
- 1998/07/13: "Morph movies" have been prepared of conformational
changes of the proteins recoverin (including a close-up of an EF hand
without and with calcium), CD11b leukocyte integrin (MIDAS adhesion
site), and influenza hemagglutinin. These are presented in the new Protein Morpher.
- 1998/04/22: The Noncovalent Bond
Finder has been further enhanced (now version 1.4). Previously
loaded PDB files are now remembered between sessions, you can start
at a radius of less than 2.5 Angstroms, and some other conveniences
- 1998/04/15: The Noncovalent Bond
Finder has been further enhanced (now version 1.3). One can now
add to or replace the target (with atoms or residues) by clicking
on atoms with the mouse. Many additional minor improvements were made.
- 1998/04/13: For our workshops, a quick
reference handout has been prepared listing the
RasMol/Chime Color RGB Values in decimal
and hexadecimal. This is helpful when making an HTML color key for
- 1998/04/13: The Noncovalent Bond
Finder has been further enhanced (now version 1.2). It should
crash Navigator much less (if at all), and some new capabilities
- 1998/04/09: The Noncovalent Bond
Finder has been significantly enhanced (now version 1.1).
- 1998/04/07: A Noncovalent Bond
Finder has been Developed (requires Chime 2). It contains an
introductory demonstration of how to find atom-pairs at suitable
distances for hydrogen or hydrophobic bonding. It makes finding these
bonds between chains, or chains and ligands, as easy as pushing a
button. Putatively bonded atoms are shown a few at a time (in 0.1
Angstrom shells) to avoid too many being found at once.
- 1998/04/01: A further set of improvements have been made to the
template provided to make development of a Chime presentation as easy
as possible. The template is now in
- 1998/03/11: A bug was reported today (thanks to Tim Driscoll)
in the Chime presentations
Presenting RasMol-Saved Scripts with Chime,
and the accompanying template.
The bug was introduced on February 17 or 19, 1998, when font size control
was added. It causes the fontsize-down button to disappear, and then
Netscape Navigator 3.0x to crash (both Windows 95
and Macintosh). The file fontsize.js has been modified in all
of the above to disable font size control in Navigator versions less
than 4.01, which allows the presentations to work normally otherwise.
Font size control remains functional in Navigator 4.01 or later.
If you used the template downloaded since February 17, 1998, simply
download the new version and substutute the new fontsize.js
which is the only file changed since then. Sorry, but the version numbers of
all the above presentations have not been changed with this
- 1998/02/19: Font size control was added to the presentations on
- 1998/02/17: The template for creating
Chime presentations (version 2) now supports changing the font size
in the right frame, and a few other minor enhancements. The Hemoglobin tutorial has been similarly
enhanced. Larger font sizes greatly improve legibility when these are
shown to a group. Instructions have also been provided for
adding font-size control to existing
- 1998/01/24: All UMass Chime resources are now believed to be
with Navigator 4.04 (except
Protein Secondary Structure,
- 1997/11/16: New presentation on major
histocompatibility (MHC) presentation of antigenic peptides,
including both classes I and II. Still under development but
offered as is for now.
- 1997/11/04: Dates have been set for the 1998 series of free, NSF-supported
workshops taught by Eric Martz in Amherst MA and New York City. These
enable college faculty to use molecular visualization in their teaching.
(Participants pay their own travel.)
- 1997/10/13: The
tutorial has been updated to version 1.2, which has several
- 1997/09/27: A new Chime tutorial on
by Eric Martz, ported
from his November 1995 RasMol "movie" script.
- 1997/09/21: A new Chime tutorial on
ported by Rashie Athukorala and Eric Martz
from the March 1996 RasMol "movie" script by Eric Martz.
- 1997/07/25: The nonlinear DNA Structure Tutorial
has been enhanced and made compatible with Netscape Navigator 4.01.
- 1997/07/25: New more complete
browser compatibility table for the Chime
resources at this site.
- 1997/07/10: New template provides the
simplest way yet to build
a presentation in Chime,
using RasMol-saved scripts.
- 1997/06/15: Button backgrounds in the
DNA tutorial were changed from black to gray to make
it easier to see the mouse pointer.
- 1997/05/13: The command line
interface demonstration for Chime was improved, and a bug
was noted which affects Macintosh users.
- 1997/04/07: A new World Index to
Educational BioMolecular Structure Tutorials in Chime and RasMol
has been linked to a newly restructured page on
BioMolecules in the
- 1997/03/21: Free workshops for college
bioscience faculty in the northeastern USA announced today for
- 1997/03/14: Netscape Communicator preview
release 2 (4.0b2) does NOT work with the UMass Chime tutorials at this
site. (Thanks to Goran Eriksson for bringing this to my attention.)
- 1997/03/12: Henry Brzeski has ported
his earlier RasMol script on lac repressor
interactions with DNA.
- 1997/02/06: Testing on Macintosh and SGI reveals
problems which will take a while to fix.
- 1997/01/28: New link to excellent Chime tutorials on
HIV-1 protease, p53 tumor suppressor, protein kinase C, the crossovers
of flavodoxin of Anabaena, cyclooxygenases vs. aspirin/NSAID's, and G
by Edward K. O'Neill and Charles M. Grisham of the
University of Virginia, Charlottesville.
- 1997/01/21: The DNA Structure Tutorial
has been enhanced and much more thoroughly documented. Toggle hydrogen
atoms on single base pairs, see hydrogen bonds in more detail, and see
double bonds. A development/debugging mode has been implemented.
- 1997/01/02: The tutorial on Protein
Secondary Structure has been greatly improved to match the
capabilities of Chime 1.0. The new version is presented with Linear
Control Structure version 2 (LCS2) for Chime presentations,
LCS2 can be used to present any linear Chime script.
Chime 1.0 released!!!
- 1996/12/10: New and improved example of how to include a
command-line interface in
a Chime web page while it is under development.
- 1996/12/2: Provided
example of Chime's ButtonCallback
Creating Chime Web Pages).
- 1996/11/30: "Further Resources ... " added to the tutorial
on Protein Secondary Structure. Added
mention of printing and exporting GIF images under
Advantages of RasMol.
- 1996/11/25: All Chime resources at this site are now
available to be downloaded
for fast operation from your local hard disk without an Internet
connection (e.g. for projection in a class) and for examining the methods used.
- 1996/11/16: See the new document
How Chime Works. Minor improvements were made to most other documents.
- 1996/11/10: "Creating Chime Web Pages" has been fixed. It
was crashing Netscape because I had inadvertantly ftp'd the PDB files
in ASCII mode, when in fact they had been gzipped and therefore required
binary transfer. A word to the wise ...
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