Molecular Modeling with Java3d & VRML on Linux

The "Java Molecular Viewer" (JMV) is a molecule viewer program written in Java and Java3D developed by the NIH ( the US National Institute Of Health ). It is designed to be an easy-to-use, platform neutral molecular visualization tool which can be used standalone or integrated into a larger program. It provides several molecular representations, multiple coloring styles, lighting controls, and stereoscopic rendering capabilities. It loads VRML and PDB files over the web, from the RCSB protein databank, from BioCoRE filesystems, and from local filesystems. http://freshmeat.net/projects/jmv/ Run the Demo   Java3d required

Java Source Code is available:   Download here For additional information see the JMV page at the Theoretical and Computational Biophysics Group

Virtual Chemistry Lab implemented with VRML, Java3d, XML, with the Sun VRML Loaders

3d VRML Modeling   with Animation on Linux ( Red Hat 7.2 ):   7 instances of my Java3d VRML Viewer program

Your browser is not configured to run Java !

Gallium Arsenide Crystal   ( Java enabled browser required )

  
 3D Solid State Crystals models ( VRML & some with Java )
 -------------------------------------------------------
 http://www.ipm.sci-nnov.ru/~demidov/VRML/cryst/cryst.htm
 http://www.ipm.sci-nnov.ru/~demidov/VRML/cryst/Mview/Packed.htm
 http://www.ipm.sci-nnov.ru/~demidov/VRML/Kat/GaAs.htm
 http://www.ipm.sci-nnov.ru/~demidov/VRML/cryst/GaAs.wrl
 http://www.ipm.sci-nnov.ru/~demidov/VRML/cryst/GaAs.jpg

 http://www.ipm.sci-nnov.ru/~demidov/VRML/cryst/Mview/ 
 http://www.ipm.sci-nnov.ru/~demidov/VRML/cryst/Mview/models/GaAs.xyz
 http://www.ipm.sci-nnov.ru/~demidov/
 Dr. Evgeny Demidov

  http://www.frontiernet.net/~imaging/shout3d/models/molecule_GaAs.wrl


 "Scientific, Engineering, and Mathematical VRML Worlds"
 ------------------------------------------------------
  Robert Lipman, NIST, Computer-Integrated Construction Group
 
  http://cic.nist.gov/lipman/sciviz/random.html
  http://cic.nist.gov/lipman/sciviz/
  http://cic.nist.gov/lipman/vrml/
  http://cic.nist.gov/lipman/vrml/hitdensity.wrl



Our Solar System : Hierarchical Motion Explained
 ( Planetary System of Sun, Earth & Moon ) by Sandy Ressler
------------------------------------------------
 Sandy Ressler is Web3d's Vice-President, a "Guide" for "about.com"
and his 'day job' is at the NIST, exploring modeling & simulations
with computers, and Lego blocks:

 |
 http://3dgraphics.about.com/library/graphics/101800b.wrl
 |
 http://3dgraphics.about.com/library/weekly/aa101800a.htm  


 Molecular Modeling with VRML
 ----------------------------
  http://atom.princeton.edu/donev/Packing/VRML/
  http://atom.princeton.edu/donev/Packing/VRML/Random.3.3D.500.wrl
  http://atom.princeton.edu/donev/Packing/VRML/SpherePackings.wrl
  http://atom.princeton.edu/donev/
 
  VRML considerations:  " Rigidity of Hard Sphere Packings " 
 |--------------------------------------------------------
 |
 | This ... requires that you use a Windows [ VRLML ] viewer.
 | This is because the main VRML code contains some complex 
 | JavaScript which I have not yet gotten to work with any 
 | of the (few) Linux VRML viewers. I am in the process of 
 | converting these to Java3D. Also, I can not offer you 
 | snapshots or MPEG replacements because these Windows 
 | plugins are not made for scientists...
 |
 | [ Note: I think this is best done with Java3d. -- Paul ]
 |
 http://atom.princeton.edu/donev/Packing/
 |
 +--  Aleksandar Donev,   Princeton University

 Yo, Aleksandar: 
 
  Java3d is made for scientists ( and the web ).

  I can make movies from my VRML files and animations
  with Java3d using the Java Media Framework ...
  and you can too.  Why not ... get with the times and
  program in Java instead of Javascript, and use 
  Java3d ( instead of the VRML plug-ins ). It was
  designed to run on Linux, SGI, HP-UX, IBM AIX & etc.
  and it was designed for:  Scientists, Programmers,
  and heavy duty 'industrial strength' animation tasks.


 Earth Model from Nasa's Goddard Space Flight Center
 -----------------------( shown above, see "URGENT" below )
 |
  http://fdab1.gsfc.nasa.gov/fdtools/default.html 
  http://fdab1.gsfc.nasa.gov/tools/web_index.asp
  http://fdab1.gsfc.nasa.gov/fdtools/vrml/fdtool.wrl
 |
 ( VRML with plug-in with propeitary extensions )

 Note: The requires plug-ins & may be sub-optimal:
 
 |  Microsoft VM & EAI with Cortona - URGENT
 | -----------------------------------------
 |
 | I have a huge problem at the moment and 
 |
 | I need a quick response if at all possible !
 |
 | I have had a tool up for over a year now and 
 | have just discovered that the latest 
 | Microsoft VM  will not work with ...
 | 
 | My code has not changed at all ...
 |
 | I am stuck on how to resolve this and
 | our client is demo'ing this tool at a 
 | NASA workshop very soon. ... Please help!
 |
  http://www.web3d.org/www-vrml/hypermail/2001/12/0186.html
 | 
  Oops, to avoid that type of problem stay with 
  portable, reliable standards: VRML & Java.

  They were made to be portable across machines, and time.

 3d Earth with Java ( @ NASA ) requies Javascript & pop-ups.
 -------------------
 http://liftoff.msfc.nasa.gov/RealTime/JTrack/3D/JTrack3D.html 
 http://liftoff.msfc.nasa.gov/RealTime/JTrack/3D/AppletFrame.html

 
 morphing fish animation with blaxxun3d ( java & vrml )
 -----------------------
 http://www.toucan.co.jp/pic/aquarium/Kawamasu0.html
 http://www.toucan.co.jp/pic/aquarium/Kawamasu0.wrl

 

  Imaging the Imagined :    Modeling with Math & a Keyboard

• Interactive 3d  with  Java3d and Sun's VRML Loaders
• Games  in  3d   with  Java3d & VRML   on Linux ( SGI, etc ) & Windows

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Last modified: 04/02/2003 First Created: 01/24/2002

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