[Molvis-list] FirstGlance in JSmol released

Eric Martz emartz at microbio.umass.edu
Sun Jan 5 19:49:10 EST 2014

I have today released a new version (1.98) at


This version uses (by default) the latest version of the SIGNED Jmol 
Java applet. This is because Oracle (who makes Java) has warned that 
unsigned Java applets will be prohibited later this month.

You may have to OK several security warnings to permit the SIGNED 
applet to operate.

This version can also be operated in the newer JSmol (notice the 
"S"), which works without Java. Performance in JSmol is not as good 
as Jmol: everything is a bit slower, rotation is slower and jumpier, 
large molecules (several thousand atoms) and 20-model NMR ensembles 
are more than it can handle. But you don't need Java, and for most 
proteins of modest size it is perfectly fine.

Theoretically this means that it should work on an iPad (where Java 
is not available) but in my preliminary quick test, Safari vaporized 
a couple of seconds after the molecule appeared. To be investigated 
later. Proteopedia.Org already works very well on iPads using JSmol.

If you start FirstGlance from a link that specifies a particular 
molecule (such as the links in Nature) for example


it will default to Jmol/Java, but you will see a prominent "Try 
FirstGlance without Java" link. That link will disappear 
automatically if loading is successful, but you can get it back by 
clicking on "No Java?" or "Can't see the molecule?".

Or you can add &nojava or &html5 (equivalent), e.g.

I have tested it in MAC OS 10.6.8 and OS 10.8.5 in Safari, Firefox, 
Chrome, Opera; and in Windows 7 in Internet Explorer 11, Firefox, 
Chrome, Opera. All work with both Jmol and JSmol.

Internet Explorer 11 is unusably slow with JSmol, so in that case, a 
yellow banner appears urging you to use another browser.

I am very impressed with how well JSmol works! Major, major kudos to 
Bob Hanson and everyone who has contributed to it!!

I welcome bug reports or comments/feedback.


/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://Martz.MolviZ.Org

Top Five 3D MolVis Technologies http://Top5.MolviZ.Org
FirstGlance: 3D Views in Nature Structure - http://firstglance.jmol.org
3D Wiki with Scene-Authoring Tools http://Proteopedia.Org
Biochem 3D Education Resources http://MolviZ.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://atlas.molviz.org
Interactive Molecules in Public Spaces http://MolecularPlayground.Org
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