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

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