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.)

2024 (dates are given year/month/day)

• 2024/08/14
  Version 4.3 of FirstGlance in Jmol released:
  • Many unique capabilities and conveniences of FirstGlance have been listed. These are not available in PyMOL, ChimeraX, or in the Mol* viewer offered at the Protein Data Bank.
  • Spreadsheet-ready lists for sorting & averaging are easily generated. These include conservation levels from ConSurf. You can list atoms engaging in Contacts & Non-Covalent Interactions, all Salt Bridges, atoms found using the Find.. dialog, and more. Examples.
  • It has long been easy to make animations for slides. New instructions are provided (with examples) for capturing movies or brief animations (GIFs) of complex operations conducted with the mouse.
  • When backbones fork due to alternate locations, the various backbone pathways can be animated. (Previously, only sidechain alternate locations could be animated.)
  • Much new documentation has been provided, including a new YouTube video about protein crosslinks.
  • Dozens of bugs were fixed.

2023 (dates are given year/month/day)

• 2023/11/09
  • Maintenance was done on the main MolviZ.Org page and on the Top 5 page. Obsolete material was removed, broken links were fixed, text and links were updated where needed. Below on this What's New page were added releases of new versions of FirstGlance in Jmol from 2020 forwards.

  2022 (dates are given year/month/day)

• 2022/09/18
  Version 4.1 of FirstGlance in Jmol released:
  • 3 minor improvements were made and 6 bugs were fixed.
• 2022/08/15
  Version 4.0 of FirstGlance in Jmol released:
  • The biological unit is now displayed initially, instead of the asymmetric unit. Examples.
  • Very large assemblies are automatically simplified to backbone atoms (alpha carbons and/or nucleic acid phosphorus atoms), or subsets of backbone atoms. This shows the large-scale structure, while reducing the number of atoms to a number manageable by JSmol. Demonstrations.
  • New color schemes were implemented in the Solid view (Views tab). Notably, each group of sequence-identical chains can be assigned a single color, and large structures, such as virus capsids, can be colored in a rainbow series ranging from from closest to the center of the structure, to farthest from the center. Illustrations.
  • Slabs, or half-structures, can now rotate. Sample animation.
  • A scale bar is now present, automatically adjusting with zooming.
  • Hiding and isolating can now operate on all sequence-identical chains in one step.
  • When a PDB code entry is not available, FirstGlance now tells you its status: on hold, withdrawn, or superseded.
  • A total of 31 improvements and bug fixes.
• 2022/01/22
  Version 3.8 of FirstGlance in Jmol released:
  • Improved documentation for distinguishing genuine protein crosslinks from clashes, with illustrated examples, as well as a more detailed description of the detection methods.
  • Numerous improvements in the handling of ConSurf evolutionary conservation results, and additional documentation.
  • A total of 34 improvements and bug fixes.

2021 (dates are given year/month/day)

• 2021/10/21
  Version 3.7 of FirstGlance in Jmol released:
  • Improvements to the handling of AlphaFold- and RoseTTAFold predicted models.
  • A total of 16 improvements and bug fixes.
• 2021/09/01
  Version 3.6 of FirstGlance in Jmol released:
  • AlphaFold- and RoseTTAFold predicted models are now handled, including new color schemes indicating the Reliability Estimates per residue.
• 2021/08/19
  • Version 3.5 of FirstGlance in Jmol released:
    • Default now shows fewer details, with an option to show more details.
    • A new YouTube video with an introduction to use of FirstGlance, and its design goals, presented and narrated by the author of FirstGlance, Eric Martz.
    • Protein crosslinks. Six types of covalent crosslinks between polypeptides are now automatically detected and reported: isopeptide, thioester, thioether, ester, histidine-tyrosine, and lys-cys NOS bonds (the latter first recognized in 2021).
    • Electron density maps can now be displayed (with explanation of how to use them) for models determined by X-ray diffraction, and density maps for electron microscopy.
    • A total of 39 improvements and bug fixes.

2020 (dates are given year/month/day)

• 2020/08/19
  • Added a new top row featuring new tutorials on Coronavirus Spike Protein Priming, Membrane Fusion by Coronavirus Spike Protein, and featuring an existing earlier tutorial on Influenza Neuraminidase, Tamiful and Relenza.
• 2020/07/17
  • A narrated YouTube video of the Java-dependent Major Histocompatibility Complex tutorial has been prepared. This will make it available until the tutorial is rebuilt to remove the Java requirement.
• 2020/07/06
  • A narrated YouTube video of the Java-dependent Antibody tutorial has been prepared. This will make it available until the tutorial is rebuilt to remove the Java requirement.
• 2020/04/03
  • Version 3.0 of FirstGlance in Jmol released:
    • All salt bridges can be listed spreadsheet-ready.
    • Amino and carboxy terminal charges are now included in salt bridges, and amino termini in cation-pi interactions.
    • Dipeptides are now included in Ligands+ in accordance with wwPDB specifications.
    • D-amino acids handled correctly.
    • New Animation Kit for more control making presentation-ready animations.
    • New instructions for aligning protein sequences and displaying the results.
    • A total of 54 improvements and bug fixes.

  2019 (dates are given year/month/day)

• 2019/01/29
  • Fixed links to the Lipid Bilayer and Water tutorials that were unnecessarily instructing users about Java (no longer needed).
  • Under "Jmol Tutorials Elsewhere", added 3 more links under Proteopedia.

  2018 (dates are given year/month/day)

• 2018/09/26
  • Fixed broken link to Molecular Sculpture.
• 2018/08/28
  • The Hemoglobin Tutorial no longer requires Java. This is its first update in 11 years. There are additional views and new morphs. Its history traces back through the Jmol Java applet, Chime, to its birth in 1996 as a RasMol movie script. Videos have been captured of its earlier incarnations.
• 2018/05/30
  • Added new tutorial: Ramachandran Principle, Phi/Psi Angles, & Clashes.
  • Added new section on Molecular Sculpture.
  • All BioModel resources are now available in JSmol.

  2016 (dates are given year/month/day)

• 2016/7/17:
  • Updated several areas of the main page.
  • Several existing resources newly use JSmol (Water, Periodic Table).
  • Added a new collection of Protein 3D Structure Resources for Educators
  • Polyview-3D has been de-emphasized since presentation-ready animations can now be saved directly from FirstGlance in Jmol. However, FirstGlance does not support customization of the molecular view, so Polyview-3D is still the easiest way to customize an image or animation.
  • The tutorials formerly offered with Lehninger's Biochemistry have been discontinued.
• 2016/5/31:
  • A new version of FirstGlance in Jmol is able to save presentation-ready animations and still images.
• 2016/2/22:
  • Major updates to the Atlas of Macromolecules.
• 2016/2/6:
  • Repaired broken links to Lipid bilayers and gramicidin channel.

  2015 (dates are given year/month/day)

• 2015/4/29:
  • 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)

• 2014/8/3-5:
  • 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 utilizing the defunct plugin MDL Chime, and documentation about Chime.
    • Protein Explorer.
    • World Index of Molecular Visualization Resources (broken since January 2012).
  • Tutorials and resources utilizing JSmol were marked JSmol.
  • Instructions were provided for enabling Java in order to use tutorials that still depend on the unsigned Jmol applet (markedJmol).

  2013 (dates are given year/month/day)

• 2013/4/13:
  • 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)

• 2010/9/9:
  • 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)

• 2008/5/3:
  • Added tutorial on Antibody in Jmol, ported by Frieda Reichsman from the earlier Chime version.
  • Added Proteopedia.Org to the main page and to Top 5.
  • 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 Herráez.
  
  
• 2007/8/4: Added a new page describing the MolviZ Top 5, and linked it to MolviZ.Org
  
  
• 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 (BioModel) and Frieda Reichsman (MoleculesInMotion.Com) 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 for Chime on the 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, molviz.css, molviz.js.)
  
  
• 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) linked to MoleculesInMotion.Com. 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 entry. Details.
  
  
• 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. Links at MoleculesInMotion.Com.
  
  
• 2007/4/16: Our hemoglobin tutorial, available in Chime since 1997, is now 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 the Pepitope Server, which predicts antibody epitopes (including discontinuous epitopes) on a 3D protein antigen, based on the sequences of peptides that bind to the antibody.
  
  
• 2007/1: 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 (biomodel.uah.es). Frieda Reichsman (MoleculesInMotion.Com) is the lead developer in this project.
  
  
• 2007/1-6: One-day, hands-on workshops on protein molecular visualization and structural bioinformatics (workshops.proteinexplorer.org) 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, and 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 workshops.proteinexplorer.org.

  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 (see History). Because of its significance, the journal has made this paper and the figures in Jmol available free to non-subscribers -- see MoleculesInMotion.Com.
  
  
• 2006/12/10: FirstGlance in Jmol (firstglance.jmol.org) version 1.0 released with What is FirstGlance in Jmol and instructions for putting static snapshots of molecular views into presentations. Details..
  
  
• 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.
  
  
• 2006/7: Biomolecules in the computer: Jmol to the rescue by Angel Herráez (biomodel.uah.es) appeared in Biochemistry and Molecular Biology Education. Jmol (jmol.org) is rapidly superceding Chime for many compelling reasons. Other Jmol literature is in the Jmol Wiki.
  
  
• 2006/6/20: Protein Explorer 2.78 Beta released (proteinexplorer.org) with 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 documentation, etc. Details.
  
  
• 2006/6/18: 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 downloaded as a single PDB file. See What's New in ConSurf 3?.
  
  
• 2006/5/10: FirstGlance in Jmol (firstglance.jmol.org) 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 (firstglance.jmol.org) 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 (firstglance.jmol.org) 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 (firstglance.jmol.org) 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) is now available on CD to facilitate use in classrooms with slow (or no) Internet connections.
  
  
• 2005/07/24: Released Protein Explorer 2.76 Alpha, with many improvements in management of MolSlides.
  
  
• 2005/06/12: Released Protein Explorer 2.75 Alpha, which introduces MolSlides.Org, and 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.
  
  
• 2005/06/10: BioMolecular Explorer 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. Go to proteinexplorer.org 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 building PiPEs. Go to proteinexplorer.org 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. Go to proteinexplorer.org 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 Martz.
  
  
• 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 at proteinexplorer.org. 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)

• 2004/12/22: 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 within proteinexplorer.org.

• 2004/11/01: Moved the former "RasMol email list" to a new home: molvis-list at bioinformatics.org.

• 2004/10/03: Released a 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 within proteinexplorer.org.

• 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 2.41 Beta.

• 2004/08/15: Linked Max Perutz interview movies to the 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. (Details.)

• 2004/06/10: Protein Explorer 2.25 Alpha translation to 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. (Details.)

• 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. (Details.)

• 2004/03/21: Updated, expanded and reorganized the section About Chime at the bottom of the main page, the title of which was also updated. Updated What Is Chime? and Chime: Browsers, Platforms, Installation, Troubleshooting. Created two new documents: How to Download & Install Free MDL Chime and 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)

• 2003/12/10: 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 proteinexplorer.org. 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 full details.
• 2003/02/15: A new site was released on Toobers in 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 proteinexplorer.org) 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 in 1E3M (3rd item under "Challenging").
• 2002/08/30: Protein Explorer 1.98 Beta released (access via proteinexplorer.org). 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 Protein Explorer.
• 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 San Diego.
• 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 auf Deutsch, thanks to Franz Josef Scharfenberger, Richard-Wagner-Gymnasium, Bayreuth. Thanks to Gonzalo Claros, U. Malaga, available en Español are the 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. See What's New? for full details.
• 2001/08/04: Gonzalo Claros (University of Malaga) has translated the tutorial on DNA structure into Spanish!
• 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 Spanish!
• 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 added.
• 2001/02/04: The antibody tutorial has been improved.
• 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

• 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 minor improvements.
• 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 Explorer.
• 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 was revised.
• 2000/08/26: A new presentation is available that shows knots 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.
• 2000/08/01: 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.
• 2000/05/22: 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 Protein Morpher.
• 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

• 1999/11/??: Protein Explorer 1.0 made available at the Protein Data Bank.
• 1999/10/06: Protein Explorer 1.0 made available at the beta 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 parameter, e.g. http://www.umass.edu/microbio/chime/explorer/pe.htm?id=1b07) 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 chime-feedback@mdli.com.
• 1999/05/20: 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 downloaded.
• 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 to the 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

• 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 were added.
• 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 Chime's colors.
• 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 were implemented.
• 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 version 2.4.
• 1998/03/11: A bug was reported today (thanks to Tim Driscoll) in the Chime presentations on Antibody, MHC, Hemoglobin, 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 bug workaround.
• 1998/02/19: Font size control was added to the presentations on Antibody and MHC.
• 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 Chime presentations.
• 1998/01/24: All UMass Chime resources are now believed to be compatible with Navigator 4.04 (except Protein Secondary Structure, which see).

  1997

• 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 Antibody tutorial has been updated to version 1.2, which has several enhancements.
• 1997/09/27: A new Chime tutorial on Antibody, by Eric Martz, ported from his November 1995 RasMol "movie" script.
• 1997/09/21: A new Chime tutorial on Hemoglobin, 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 Classroom.
• 1997/03/21: Free workshops for college bioscience faculty in the northeastern USA announced today for summer, 1997.
• 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 to Chime 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 proteins 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, comprising >1,000 lines of javascript plus >750 lines of html. LCS2 can be used to present any linear Chime script.

  1996

• 1996/12/31: 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 mechanism (under 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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