Files Description - Revision history

AngelHerraez: /* Files of the Jmol object */

2025-08-12T10:49:49Z

‎Files of the Jmol object

AngelHerraez: /* Files of the Jmol object */

2025-08-12T10:49:22Z

‎Files of the Jmol object

AngelHerraez: Updating for Jmol 16. All previous history (until some 14.x version of Jmol) is kept at the page Files_Description/Jmol_14

2024-04-18T15:24:05Z

Updating for Jmol 16. All previous history (until some 14.x version of Jmol) is kept at the page Files_Description/Jmol_14

AngelHerraez: Updating for Jmol 16. All previous history (until some 14.x version of Jmol) is kept at the page Files_Description/Jmol_14

2024-04-18T15:12:25Z

Updating for Jmol 16. All previous history (until some 14.x version of Jmol) is kept at the page Files_Description/Jmol_14

New page

'''''For Jmol versions previous to some 14.x, see [[Files_Description/Jmol_14]]'''''



The Jmol distribution is available for download as 3 different files:
* {{File|jmol-x.x.x-binary.zip}} contains all files needed for using Jmol, compressed using the <code>zip</code> format.
* {{File|jmol-x.x.x-binary.tar.gz}} contains the same files, in a <code>tar</code> structure and compressed using the <code>gzip</code> format.
* {{File|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_Documentation_Sections}}

== 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.

<br>
== 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 [[Jmol_Application#Command_line_options|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 {{file|jmol.sh}} script:<br>
(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 {{file|$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 {{file|jmol-xxx}} folder to {{file|/usr/bin/}} or {{file|/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

<br>
== 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 [[Jmol_Application#Starting_Jmol_Application|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.

<br>
== 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]]

@@ Line 90: / Line 90: @@
 * 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 [[JavaScript Object/Installation]]
+For details on the files contained, their purpose and how to use them, please see [[Jmol JavaScript Object/Installation]]
 <br>

@@ Line 90: / Line 90: @@
 * 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]]
+For details on the files contained, their purpose and how to use them, please see [[JavaScript Object/Installation]]
 <br>
 == Other files  ==
 === JSpecView.jar ===
 This is an application executable file (a program written in Java) for JSpecView, a viewer for spectra which may be interconnected with Jmol. https://jspecview.sourceforge.net/   https://sourceforge.net/projects/jspecview/

@@ Line 20: / Line 20: @@
 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 ===
+=== buildREADME.txt ===
-The Spanish version of README.txt
+Information for how to build the Jmol package (for developers).
 === CHANGES.txt ===
@@ Line 81: / Line 82: @@
 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".
 <br>
@@ Line 93: / Line 91: @@
 For details on the files contained, their purpose and how to use them, please see [[Jmol_JavaScript_Object#Installation]]