Jmol Application

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Revision as of 20:27, 10 January 2011 by EricMartz (talk | contribs) (→‎Giving Jmol more memory to work with)
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Reference: English – Other: 日本語 ·

Running Jmol / JSmol

Jmol Application

"Jmol Application" is the version of Jmol that runs as a standalone program, in its own window. The program code is written using the Java programming language, therefore to be run it needs an installed Java Virtual Machine (a runtime version of Java, or JRE); this JVM is available for all major operating systems, including Windows, MacOS and Linux.

Jmol Application window

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 the 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

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

See also specific tips in Support/Linux, Support/OS X, Support/Windows, for example how to create a Mac OSX native installer.

To open the application, follow these instructions:

Starting Jmol Application

Several ways:

  • Double-click on File icon.gifJmol.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 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.

If you have trouble running the application, see also Troubleshooting.

If you want to attach a Jmol icon to your preferred method of opening Jmol, you can get one from the Recycling Corner.

See also specific tips in Support/Linux, Support/OS X, Support/Windows, for example how to create a Mac OSX native installer.

Command line options

Note: For all the following, calling directly 

Jmol.jar (some options)

will only work as long as the File icon.gif.jar files are associated with Java. Otherwise, the general syntax for all cases is 

java -jar Jmol.jar (some options)

but the 'java -jar' part will be omitted for simplicity (except where it is unavoidable).

In fact, you can also just use 

Jmol (some options)

provided you have in the same folder/directory the batch file or shell script adequate for your OS (included with Jmol distribution).

Basic options

  • To show help for command-line options, use either of these:
java -jar Jmol.jar -h
java -jar Jmol.jar --help
  • To load a molecular file immediately after opening Jmol, use:
Jmol.jar  fileName
  • To run a script file immediately after opening Jmol, use:
Jmol.jar  scriptFileName
  • You can combine loading a molecular file, running a script file and running script commands (only Jmol 11.7.x and later):
Jmol.jar  fileName  -J script_commands  -s scriptFileName  -j script_commands
which will be run in that order irrespective of their actual order in the command line. Either of the 4 may be omitted. Case of the "-J" is significant when combined with "-s".
  • To set the application's window size, use either of these:
Jmol.jar -g  WIDTHxHEIGHT 
Jmol.jar --geometry  WIDTHxHEIGHT
using lowercase 'x' and no spaces, e.g. Jmol.jar -g 500x250. By default, size is the last size used or else 500x500.
Jmol.jar -m fileName 
Jmol.jar --menu  fileName
  • To set the language to be used for the interface, use:
java -Duser.language=ca|cs|de|en_GB|en_US|es|fr|hu|it|ko|nl|pt_BR|tr|zh_TW  -jar Jmol.jar
(default is the language of the operating system or else, if that is not available, en_US; see also).
  • To report the display speed in either frames per second or milliseconds per frame (the default), use:
java -Ddisplay.speed=fps|ms  -jar Jmol.jar
  • To set a path where to look for plugins for Jmol, use:
java -Dplugin.dir=/path/to/plugins   -jar Jmol.jar
  • To specify 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 (i.e. 512 MB maximum).

xxx

See also the procedure for the applet.

Advanced options

  • To avoid the splash screen from being displayed, use either of these:
Jmol.jar -L
Jmol.jar --nosplash
  • To open the app with a transparent background (may not function, use at your own risk), use either of these:
Jmol.jar -b
Jmol.jar --backgroundtransparent
  • To have Jmol export a snapshot of the rendered model to an image file, use either of these:
Jmol.jar fileNameToLoad -w imageFormat:imageFileName 
Jmol.jar fileNameToLoad --write imageFormat:imageFileName 
Jmol.jar -s scriptFileNameToLoad -w imageFormat:imageFileName 
Jmol.jar --script scriptFileNameToLoad --write imageFormat:imageFileName
Where imageFormat may be one of these (and must be followed by a colon): JPG , JPEG , JPG64 , PNG , PPM , or CLIP for copying the image to the clipboard instead of writing to a file.
  • To set the quality of images written to file, use either of these:
Jmol.jar fileNameToLoad -q## -w imageFormat:imageFileName
Jmol.jar fileNameToLoad --quality## --write imageFormat:imageFileName
Jmol.jar -s scriptFileNameToLoad -q## -w imageFormat:imageFileName
Jmol.jar --script scriptFileNameToLoad --quality## --write imageFormat:imageFileName
Where the ## may be a number from 1 to 100, meaning quality of JPG (75 by default), or a number from 0 to 9, meaning compression of PNG (2 by default, 9 maximum compression).
  • To have the syntax of scripts checked, without actually executing them, use either of these:
Jmol.jar -c
Jmol.jar --check
  • To have the syntax of scripts checked and also execute them, use either of these:
Jmol.jar -C
Jmol.jar --checkload
  • To have the script commands listed while running them, use either of these:
Jmol.jar -l
Jmol.jar --list
  • To get a silent startup operation, use either of these:
Jmol.jar -i
Jmol.jar --silent
  • To have output messages put to the standard system output (e.g. the terminal), instead of to the internal Jmol Java console, use either of these:
Jmol.jar -o
Jmol.jar --noconsole
  • To avoid the use of the screen display (all rendering done only in memory, hence accelerating Jmol), use either of these:
Jmol.jar -n
Jmol.jar --nodisplay
Normally, this should be used together with other switches like -x (see below).
  • To have the application exit once finished (e.g. after running a script), use either of these:
Jmol.jar -x
Jmol.jar --exit
  • To start in debug mode, use either of these:
Jmol.jar -d
Jmol.jar --debug
  • To use an independent thread, use either of these:
Jmol.jar -t
Jmol.jar --threaded


Examples:

Create a JVXL file directly: 

 Jmol.jar -ionx myfile.xyz iso.spt > myfile.jvxl
where File icon.gifiso.spt contains:
isosurface solvent; show isosurface
will create a File icon.gifmyfile.jvxl file containing data for a solvent surface in Jmol isosurface format (JVXL).

Create a list of measurements: 

 Jmol.jar -ionx myfile.xyz measure.spt > measure.txt
where File icon.gifmeasure.spt contains:
measure allconnected (*) (*); show measurements
which generates a list of measurements. The output file, File icon.gifmeasure.txt, will contain (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.jar -ionx myfile.cif symmetry.spt > symmetry.txt
where File icon.gifsymmetry.spt contains:
   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.

Forcing Jmol to open in a certain language

Jmol includes several languages (technically called localizations) for the user interface (top menu and pop-up menu). Jmol will open by default with the interface using the language of your operating system (ref.). However, if you need to change this:

  1. Starting Jmol 11.1.30, the language in application can be switched anytime, from the pop-up menu, "Language" item near the bottom.
  2. Or, using the scripting language: language = "de" (you must use the keyword "language" and the two-letter language code: ca, cs, de, en, es, et, fr, nl, pt, tr, or four-letter code: en_GB, en_US, pt_BR, zh_TW)
  3. This is an old method, only needed for versions below 11.1.30: If you want to force a certain language, you must start Jmol with
java -Duser.language=es -jar Jmol.jar # forces Spanish (Español)
java -Duser.language=de -jar Jmol.jar # forces German (Deutsch)
java -Duser.language=en -jar Jmol.jar # forces English
etc.

See also the procedure for the applet.

Contributors

AngelHerraez, EricMartz, Pimpim, Cudo29, NicolasVervelle, Green

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