Jmol Application

Running Jmol / JSmol

• Jmol as a standalone application.
• J(S)mol as a web applet or HTML5 object.
  • compatibility with JavaScript frameworks or libraries.
• J(S)mol embedded in wikis or blogs.
• Borrowed JSmol, or running JSmol without your own server.
• Running Jmol using Java Web Start.
• JSmol in a Jupyter notebook.
• Jmol in an Android tablet.
• Troubleshooting.

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.

Installing Jmol Application

Installing Jmol / JSmol

• Get the files from SourceForge.
• Support and operating systems.
• Users: how to install Jmol application for local, standalone use.
• Web page authors: how to install Jmol objects (Jmol / JSmol) embedded within your web pages.
  • Installing and Enabling Java (Proteopedia wiki). Has step by step instructions for both Windows and Mac OS X, and for the 5 most popular web browsers.
  • Increasing java memory for the applet.
• Web site administrators:
  • How to install the application on a web server to be delivered using Java Web Start.
  • How to configure a wiki so that it uses the Jmol applet.
• Developers: compile the latest Jmol source code via subversion access.

Download Jmol package (either .zip or tar.gz format) and extract/uncompress only the Jmol.jar file to the folder of your choice.

To open the application, follow these instructions:

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).
• only for Macs, Fernanda Foertter has packed Jmol application into a clickable icon / .app type icon that opens up Jmol. This makes it look like a regular 'ol app without all of the exposed jar files. It is available at her site as a dmg file. Instructions: 1) download dmg file; 2) double-click to open; 3) drag Jmol icon to you Applications folder to install; 4) eject dmg; 5) trash dmg file; 6) double-click Jmol icon to open application, or 6a) click and drag to dock to have ready whenever needed.

Command line options

Basic options

• Show help for command-line options: use either of these:

java -h -jar Jmol.jar
java -help -jar Jmol.jar
java -? -jar Jmol.jar

• Load a molecular file: use either of these:

Jmol.jar  fileName
java -jar Jmol.jar  fileName

• Run a script: use either of these:

Jmol.jar -s  script_fileName
Jmol.jar  script_fileName
java -jar Jmol.jar  script_fileName

• Set the window size: use either of these:

Jmol.jar -g  WIDTHxHEIGHT   
Jmol.jar --geometry  WIDTHxHEIGHT
java -jar Jmol.jar  -g  WIDTHxHEIGHT   

using lowercase 'x' and no spaces, e.g. Jmol.jar -g 500x250. By default, size is the last size used or else 500x500.

• Set the language to be used for the interface (default is language of the operating system) see also:

java -Duser.language=ca|cs|de|en|es|et|fr|nl|pt|tr  -jar Jmol.jar

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

java -Ddisplay.speed=fps|ms  -jar Jmol.jar

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

java -Dplugin.dir=/path/to/plugins  -jar Jmol.jar

• Set memory use (see below):

java -Xmxsize  -jar Jmol.jar

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 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