Files Description/Jmol 14

This is valid up to some Jmol version 14.x; for later versions, see Files_Description

For Jmol versions previous to 13.2, see Files_Description/Jmol_12

The Jmol distribution is available for download as 3 different files:

• jmol-x.x.x-binary.zip contains all files needed for using Jmol, compressed using the zip format.
• jmol-x.x.x-binary.tar.gz contains the same files, in a tar structure and compressed using the gzip format.
• jmol-x.x.x-full.tar.gz contains the full source code. This will only be useful to developers and programmers wanting to study Jmol programming design or to modify Jmol.

Following is a description of the files contained in any of the first two downloadable files.

Jmol + JSmol Documentation

• 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:
    • at St Olaf (primary site)
    • at Jena3D (mirror)
• 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)

Files with information

COPYRIGHT.txt

The copyright explanations regarding Jmol and its 3rd-party components.

LICENSE.txt

The GNU Lesser General Public License, under which Jmol is released.

README.txt

A general description of Jmol package and sources of information, including this file list documentation.

LEAME.txt

The Spanish version of README.txt

CHANGES.txt

A list with a history of the feature additions in each version of Jmol.

Batch and shell files

These can be used to start Jmol application from a command line and, particularly, to impose a certain combination of parameters (see command line options).

jmol

???? (Some kind of batch file)

jmol.bat

A batch file to start Jmol application under Windows.

jmol.mac

??? (Some kind of batch file)

jmol.sh

A shell script to start Jmol application under Unix-like systems, like Linux, BSD, Solaris and Cygwin for Windows.

Under Linux, there are a number of ways to start Jmol as a standalone program using the jmol.sh script:
(1)

sh jmol.sh                      // start Jmol under the jmol-xxx folder 
sh yourpath/jmol-xxx/jmol.sh    // start Jmol from anywhere 

(2)

chmod +x jmol.sh                // make the jmol.sh script executable 
jmol.sh                         // start Jmol inside the jmol-xxx directory, or  
yourpath/jmol-xxx/jmol.sh       // start Jmol anywhere

(3)

chmod +x jmol.sh                // make the jmol.sh script executable  
ln -s yourpath/jmol-xxx/jmol.sh /usr/local/bin/jmol.sh //create a symbolic link under /usr/local/bin

Add the following shell variable in the shell script $HOME/.bash_profile

export JMOL_HOME="/yourpath/jmol-xxx/"

Reboot your computer or execute

source $HOME/.bash_profile 

Then

jmol.sh                          // start Jmol anywhere 

(4) Move the jmol-xxx folder to /usr/bin/ or /usr/local/bin/

chmod +x jmol.sh                  // make the jmol.sh script executable 
ln -s /usr/bin/jmol-xxx/jmol.sh /usr/bin/jmol.sh          // or
ln -s /usr/bin/jmol-xxx/jmol.sh /usr/local/bin/jmol.sh    // or
ln -s /usr/local/bin/jmol-xxx/jmol.sh /usr/bin/jmol.sh    //or
ln -s /usr/local/bin/jmol-xxx/jmol.sh /usr/local/bin/jmol.sh
jmol.sh                          // start Jmol from anywhere

Files of Jmol application

This is used as a standalone program.

Jmol.jar

The application executable file (a program written in Java). This works as any other program: opens in its own window, can be resized or minimized, admits drag-and-drop of files over it, has a top menu bar, can open and save files, etc. It can be open from the command line (particulary, using the shell or batch files described above), but if Java is properly configured in your system, it's usually enough to double-click on the file (see Starting Jmol Application for more details).

JmolData.jar

This is a slimmed down version of Jmol.jar that lacks all visualization capabilities. So, it betrays the whole (classic) concept of what Jmol is, but with JmolData and some clever scripting you can get just about any information you want out of a model and output it any way you want.

It operates only from the command line, designed for extracting data from a model or set of models. You are limited to commands that don't have to do with visualization: there are bonds but no "sticks", atoms but no "dots", helices but no "cartoons".

JmolLib.jar

This is a library, meant to make Jmol a module or part of a bigger project, that is, to integrate Jmol viewer inside another software.

Files of the Jmol object

jsmol.zip

This file includes in compressed form all the files for using J(S)mol inside web pages, such as:

• Applet files (for the Java modality of Jmol object)
• Javascript libraries (for the definition of the Jmol object in all cases, and specifically for the HTML5 modality of Jmol object)

For details on the files contained, their purpose and how to use them, please see Jmol_JavaScript_Object#Installation

Contributors

Zhang2010, AngelHerraez, Pimpim, NicolasVervelle