Jmol
Jmol, an free open-source Java molecule viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules.

A list of features:
  • Free, open-source software licensed under the GNU Lesser General Public License
  • Applet, Application, and Systems Integration Component
  • Multi-language
  • Automatically adopts the language of the user's operating system, if it is among the translations available. You can change to another language if desired.
  • Cross-platform
  • Supports all major web browsers: Internet Explorer, Mozilla and Firefox, Safari, Google Chrome, Opera, Konqueror, IceWeasel, ...
  • High-performance 3D rendering with no hardware requirements
  • File formats (see also the file formats section within Jmol Wiki)
  • Animations
  • Vibrations
  • Surfaces
  • Orbitals
  • Support for unit cell and symmetry operations
  • Schematic shapes for secondary structures in biomolecules
  • Measurements: distance, angle and torsion angle
  • Support for RasMol/Chime scripting language
  • JavaScript support library (Jmol.js)
  • Exports to jpg, png, gif, ppm, pdf, POV-Ray, Gaussian, Maya, vrml, x3d, idtf, web page.
  • For more details, see the history of development.

System requirements
  • Version 1.6.0 Build 27 GA5 (2013-02-17)
  • Enough memory to work with, 512Mb will do nicely


Jmol on an eComStation machine with Open JDK


Installing Jmol
Download Jmol-14.29.46-binary.zip. Create a folder (directory) "jmol". Open the zip file en go in the subdirectory "jmol-14.29.46". Copy the files in this directory to the new folder "jmol". That's it. Delete the files jmol, jmol.bat, jmol.mac and jmol.sh. I didn't experiment with jsmol.zip (very big file), another candidate for the dustbin.

The jmol.cmd file
This version of Jmol works with Open JDK in OS/2-eCS. Some menuparts are not working anymore, like the download of samples. The developer told me that in future Jmol needs a higher version of Java. So piece by piece things are not working anymore in our version of Java. I got with this version the first 4 starts a hs_err_pidxx errors. After some tries with different files it was going. I have made a jmol.cmd file with the following contents; 
@echo off
SET CLASSPATH=
set BEGINLIBPATH=[drive:java]\JAVA160160ga5\bin
set path=[drive:java]\JAVA160ga5\bin
[drive:jmol]
cd [drive:jmol]\jmol
java -Duser.home=[drive:jmol]\Jmol -Duser.language=nl -Xmx512m -jar jmol.jar 2>jmol-14-29-46-bugs.txt
I use 2 separate folders (directories), one for Java and one for Jmol with the files created by this program. The references used in the cmd file;

  • [drive: java] = drive with Java
  • [drive: jmol] = drive with Jmol

should be replaced with real drive letters. Edit and save the file "jmol.cmd" from the distribution. This file is copied to the "jmol" folder (directory). Furthermore, different paths?, adjust according to your needs. There are more options to include, go to Starting_Jmol_Application.
Create a new program object. Specify the path and file name: "[drive: jmol]\jmol\jmol.cmd". In the tabpage Session check the boxes "OS/2 window", "Running as an icon" and "Close Window to end program". In the tabpage General you can enter the name "Jmol". You find enclosed in the file a suitable OS/2 icon.

Parameters / options explained
  • The specification "-Duser.home=[drive: jmol]\Jmol" ensures that Jmol will save all necessary files in own directory instead of saving them in the home directory.
  • The specification "-Duser.language=nl" sets the language to be used for the interface. The default is en_US. In the download below its still set on Dutch, you can delete this part or update it to your language.
  • The specification "-Xmx512m" comes from the included batches for other OS systems and the wiki page above. The "-Xmx512m" indicates the maximum limit.
  • The addition "2>jmol-14-29-46-bugs.txt" ensures that errors are saved in the file "jmol-14-29-46-bugs.txt". The 2 in "2>" is not a typo! If you don't want reports then you can omit this part.

Download
In the file you can find the above command file (all driveletters are set to C:) and an OS/2 Jmol icon: jmol-ecs.zip.

revision Juli 23, 2019