From emartz at microbio.umass.edu Sun Jan 5 19:49:10 2014 From: emartz at microbio.umass.edu (Eric Martz) Date: Sun, 05 Jan 2014 19:49:10 -0500 Subject: [Molvis-list] FirstGlance in JSmol released Message-ID: <201401060049.s060nITw001376@marlin.bio.umass.edu> I have today released a new version (1.98) at http://FirstGlance.Jmol.Org 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 http://FirstGlance.Jmol.Org/fg.htm?mol=1d66 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. http://FirstGlance.Jmol.Org/fg.htm?mol=1d66&nojava 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 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 Workshops: http://workshops.molviz.org - - - - - - - - - - - - - - - - - - - - - - - - - - - */ From christoph.gille at charite.de Mon Feb 24 08:39:43 2014 From: christoph.gille at charite.de (Dr. med. Christoph Gille) Date: Mon, 24 Feb 2014 14:39:43 +0100 Subject: [Molvis-list] Need beta tester for Alignment Annotator Message-ID: Could I please ask you to test Alignment Annotator which is a web application to create interactive annotated sequence alignments for web browsers including coupled OpenAstex based 3D visualization. It is found here: http://www.bioinformatics.org/strap/AA2/ Many thanks Christoph