[Molvis-list] MolviZ.Org Updated

Eric Martz emartz at microbio.umass.edu
Wed Aug 6 10:59:03 EDT 2014

MolviZ.Org <http://molviz.org> has been thoroughly and systematically 
upgraded, and also Top5.MolviZ.Org <http://top5.molviz.org>.

Many of the tutorials there are now available in JSmol (no Java needed), 
including the tutorial on DNA double helix structure 
<http://dna.molviz.org> (thanks to Ángel Herráez!). Those are now 
clearly marked *JSmol*, and will work on recent iPads and some smart phones.

For those tutorials still using the old unsigned Jmol Java applet (now 
marked *Jmol*), step-by-step instructions have been provided for 
installing and enabling Java 
<http://proteopedia.org/w/Installing_and_enabling_Java>, in both Windows 
and OS X, for the five most popular web browsers. You are now directed 
to those instructions before you get to the actual tutorial.

Also for a long time now, both Proteopedia.Org and FirstGlance.Jmol.Org 
<http://firstglance.jmol.org> default to JSmol (no Java), but each has 
an option to use Java if desired. There are many excellent tutorials on 
specific molecules 
<http://proteopedia.org/wiki/index.php/Proteopedia:Table_of_Contents> in 

Resources that utilize FirstGlance consequently also work in JSmol (no 
Java), such as the journal /Nature/ (among others 
<http://bioinformatics.org/firstglance/fgij/adoption.htm>), evolutionary 
conservation at ConSurf, functional protein assemblies/biological units 
(MakeMultimer server), lipid bilayer boundaries for integral membrane 
proteins (Orientations of Proteins in Membranes server), and the Atlas 
of Macromolecules (Atlas.MolviZ.Org <http://atlas.molviz.org>). All of 
these are available in the /Resources/ tab within FirstGlance.Jmol.Org 
<http://firstglance.jmol.org> (except the Atlas).

Thanks to Bob Hanson for his brilliant and tireless efforts that have 
made JSmol an amazing reality!


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

  * Top Five 3D MolVis Tools: Top5.MolviZ.Org <http://top5.MolviZ.Org>
  * FirstGlance: 3D Molecules in /Nature/: FirstGlance.Jmol.Org
  * Protein 3D Structure Wiki: Proteopedia.Org <http://proteopedia.Org>
  * Education: Biochem in 3D at MolviZ.Org <http://MolviZ.Org>
  * Find Functional Patches in Proteins: ConSurf <http://consurf.tau.ac.il>
  * Atlas of Macromolecules: Atlas.MolviZ.Org <http://atlas.MolviZ.Org>
  * Interactive Molecules in Architectural Spaces:
    MolecularPlayground.Org <http://molecularplayground.Org>
  * Workshops: Workshops.MolviZ.Org <http://workshops.MolviZ.Org>

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