Support/Linux
- Description of files in Jmol+JSmol distribution
- File formats read or written by Jmol
- The Jmol scripting interface
- Scripting as a programming language
- Complete reference of scripting commands:
- Loading models directly from databases
- Mouse manual
- Default colors used by Jmol
- Atom sets predefined in Jmol
- Support for bond orders · isotopes · stereochemistry · hydrogen bonds
- Jmol as editor
- Multi-touch support
- Copying and pasting state scripts between applets.
- Backward compatibility (changes of behavior across versions)
- Features added since version 10
- Users mailing list (and a mirror)
Linux
Jmol runs without problems on Linux machines using Sun's java virtual machines, both as Applet as well as Application. Running the application has not been tried with other virtual machines or compilers, like Kaffe.
Binary Jmol Packages
Binary package are available for Debian, see Debian.
Comments/Discussion
- What I would very much like to see, is a KDE GUI for Jmol. That is, a GUI that is completely independant of Swing and thus runs with free virtual machines, e.g. Kaffe. -- Egon Willighagen
SUSE 10.2 Linux i686 (x86_64)
Couldn't get Jmol to launch with memory overflow messages from script when I've had no problems from SUSE other distros on 32 bit. The message log file showed ALERT - script tried to increase memory-limit to 20971520 bytes which is above the allowed value
Solution that worked for me after debugging as root was to launch current java binary calling jar file with user permissions in user home subdirectory: eg
/usr/lib/jvm/java-1.5.0-sun-1.5.0_update12/jre/bin/java -jar {HOME}/jmol-11.2.9/Jmol.jar
with {HOME} being your own home directory fully specified, eg /home/anuser.
I disabled launch feedback with KDE menu editor options.
Presumably the symbolic links are not where Jmol expects them in jmol.sh with jvm so there will be other solutions. ChaseKiwi
