Jmol Application

Jmol Application

"Jmol Application" is the version of Jmol that runs as a standalone program, in its own window. It uses the Java programming language.

Control of the molecular model is gained through several means:

1. The mouse (documented in Mouse Manual).
2. The application's menu and toolbar (at the top of the window), which offer
   1. File open, export, and print functionalities.
   2. A limited set of selection and rendering options, and several tools.
3. The pop-up menu (or context menu, opened by right-click or Ctrl+click on the model's panel), which offers most funcionality available and is identical to applet menu.
4. The scripting language (same used by the applet); this is available through the File > Script... menu, which opens a "script console" or command-line environment.

Starting Jmol Application

Several ways:

• Double-click on Jmol.jar file.
• Click on a previously created shortcut (Windows terminology) (HowTo).
• Click on a previously created Start menu entry (Windows terminology) (HowTo).
• Execute one of the batch files/shell scripts that are part of Jmol distribution (Windows, MacOS, Linux, Unix).
• From the command line: java -jar Jmol.jar (of course, issued from the folder/directory where Jmol.jar is, or else pointing to it with a full path). See memory options below.
• Double-click on a molecular coordinates file whose extension has been previously associated to Jmol (HowTo).

Command line options

Basic options

These are described in the application documentation. Briefly:

• Load a molecular file:

Jmol.jar fileName

• Show help:

-h  or  --help

• Run a script:

Jmol.jar -s  whatever script file

or

Jmol.jar --script  whatever script file

• Set the window size (by default, the last size used or else 500x500):

Jmol.jar -g  WIDTHxHEIGHT   

(lowercase 'x' and no spaces), or

Jmol.jar --geometry  WIDTHxHEIGHT

• Set the language to be used for the interface (default English) see also:

-Duser.language=de|en|es|fr|nl|pl

• Report the display speed in either frames per second or milliseconds per frame (the default):

-Ddisplay.speed=fps|ms

• Sets a path where to look for plugins for Jmol:

-Dplugin.dir=/path/to/plugins

• Sets memory use (see below):

-Xmxsize

Giving Jmol more memory to work with

Memory available to Jmol is determined by Java. Less or more memory can be allocated by using:
java -Xmx###m -jar Jmol.jar
where the ### must be substituted by a number in megabytes (hence the "m" after it).

Technically:

• -Xmx sets the maximum memory heap size.
• -Xms sets the minimum memory heap size.

Batch files and shell scripts included with Jmol 10.2 distribution are written to give -Xmx512m (512 Mb maximum).

Advanced options (Jmol v.11)

Create a JVXL file directly:

 Jmol -ionx iso.spt myfile.xyz > myfile.jvxl

where:

• -i,--silent silent startup operation
• -o,--noconsole no console -- all output to sysout
• -n,--nodisplay no display (much faster)
• -x,--exit run script and exit

and iso.spt is:

   isosurface solvent;show isosurface

creates a JVXL solvent surface file.

Create a list of measurements:

 Jmol -ionx measure.spt myfile.xyz > measure.txt

where measure.spt is:

measure allconnected (*) (*);show measurements

generates a list of measurements.

measure.txt now contains (tab-separated):

Measurement Information

distance 1.1217928 0.112 nm H 1 #1 C 10 #10

distance 1.4158994 0.142 nm N 2 #2 C 6 #6

distance 1.3865448 0.139 nm N 2 #2 C 7 #7

...

Check CIF file symmetry:

 Jmol -ionx symmetry.spt myfile.cif > symmetry.txt

where symmetry.spt is:

   show unitcell;show symmetry;show spacegroup;

Anything that can be "shown" can be dumped to a file this way. And anything you can get from getProperty will do the same.

Contributors

AngelHerraez, EricMartz, Pimpim, Cudo29, NicolasVervelle, Green