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| − | The Jmol [[Jmol_Application|Application]] and [[Jmol_Applet|Applet]] have a command language that | + | {{Jmol_Documentation_Sections}} |
| + | __TOC__ | ||
| + | |||
| + | The Jmol [[Jmol_Application|Application]] and [[Jmol_Applet|Applet]] have a '''command language''' that grew on the base of the [http://www.mdl.com/support/developer/chime/developer_tools.jsp command language] of [http://www.umass.edu/microbio/rasmol/index2.htm RasMol] and its browser plugin [http://www.mdl.com/ MDL Chime]. A set of commands is called a '''''command script''''', and writing such sets of commands or scripts is called '''''scripting'''''. This is the major way of controlling the display of molecules in Jmol. | ||
= Documentation links = | = Documentation links = | ||
'''Documentation of Jmol's scripting language can be found here:''' | '''Documentation of Jmol's scripting language can be found here:''' | ||
| − | * | + | * {{ScriptingDoc}} |
This is the official document. The style is encyclopedic, explaining each command in turn, as usual in reference manuals. | This is the official document. The style is encyclopedic, explaining each command in turn, as usual in reference manuals. | ||
| + | In addition to this primary site, with latest updates, there are some mirror sites (see links at right). | ||
'''An introduction to Jmol scripting is available here:''' | '''An introduction to Jmol scripting is available here:''' | ||
* http://www.callutheran.edu/Academic_Programs/Departments/BioDev/omm/scripting/molmast.htm | * http://www.callutheran.edu/Academic_Programs/Departments/BioDev/omm/scripting/molmast.htm | ||
A more user-friendly, but less thorough, basic guide by Nathan Silva and David Marcey; part of the Online Macromolecular Museum at California Lutheran University. | A more user-friendly, but less thorough, basic guide by Nathan Silva and David Marcey; part of the Online Macromolecular Museum at California Lutheran University. | ||
| + | |||
| + | '''Other''' | ||
| + | * Scripts can be included inside the molecular model file. See [[File_formats/Scripting#Script_inline_within_a_molecular_coordinates_file|how to do it]]. | ||
| + | * Jmol scripting language has grown, among other features, by adding mathematical operators (''JmolMath''), control structures (loops, conditionals, etc.). You may be interested in this [[Scripting/Programming_Language|programming language]] approach. | ||
= Similar but different scripting languages = | = Similar but different scripting languages = | ||
| Line 15: | Line 23: | ||
Chime's command language (see "About Chime" at http://molviz.org) is a superset of the [http://www.umass.edu/microbio/rasmol/getras.htm#rasmanual command language] of Roger Sayle's public domain application [http://www.umass.edu/microbio/rasmol/index2.htm RasMol]. (The command language of [http://www.rasmol.org/ open-source RasMol] has diverged somewhat from that in RasMol and Chime). The command language used by Jmol started with most of the Chime commands, but has outgrown it in a notable extent, allowing for many new capabilities. | Chime's command language (see "About Chime" at http://molviz.org) is a superset of the [http://www.umass.edu/microbio/rasmol/getras.htm#rasmanual command language] of Roger Sayle's public domain application [http://www.umass.edu/microbio/rasmol/index2.htm RasMol]. (The command language of [http://www.rasmol.org/ open-source RasMol] has diverged somewhat from that in RasMol and Chime). The command language used by Jmol started with most of the Chime commands, but has outgrown it in a notable extent, allowing for many new capabilities. | ||
<pre> | <pre> | ||
| − | *-RasMol (v | + | *-RasMol (v≤2.6) |
| + | | | ||
| + | |----Chime Takes nearly all RasMol 2.6 commands and adds a few. | ||
| + | | | | ||
| + | | ----Jmol (v≥10) Takes many RasMol 2.6 and Chime 2.6 commands and adds a few. | ||
| + | | | | ||
| + | | ---Jmol (v≥11) Adds many new commands. | ||
| + | | | ||
| + | -----OpenRasMol (v≥2.7) Takes all RasMol 2.6 commands and adds a few. | ||
| + | </pre> | ||
| + | |||
| + | == RasMol commands not accepted by Jmol == | ||
| + | These are some RasMol / OpenRasMol commands that are not accepted by Jmol (they will raise an error and will stop further execution of the script): | ||
| + | * <code>set cartoon on</code> defines that cartoon display should use arrowheads -- not needed in Jmol, since that is the default (and not changeable). | ||
| + | * <code>set cartoon N</code> defines the "depth" (i.e. thickness) of the ribbons; more or less similar to Jmol's <code>cartoon N</code>. | ||
| + | * <code>color atom cpknew</code> "cpkNew" is a color scheme for elements slightly diferent than the old default "cpk"; not available as such in Jmol. See [http://jmol.sourceforge.net/jscolors/index.en.html#Atoms%20(%27CPK%27%20colors,%20default%20element%20colors) Jmol Colors] for a comparison. | ||
| + | |||
| + | = Transversal documentation = | ||
| + | Covering specific aspects or applications (not by command, and usually not exhaustive): | ||
| + | * [http://jmol.sourceforge.net/docs/surface/ Surfaces]. Jmol can calculate and render surfaces around a molecule, or part of it, representing its "true" shape and volume. Moreover, isosurfaces, atomic and molecular orbitals, and mathematically defined surfaces can also be rendered. An ''introductory'' tutorial on creating macromolecular Jmol surfaces is available: [http://www.callutheran.edu/Academic_Programs/Departments/BioDev/omm/surfaces/surfaces/surfaces.htm An Introduction to Jmol Surface Displays], part of the Online Macromolecular Museum at California Lutheran University. | ||
| + | * [[Persistent Parameters|Persistent and nonpersistent "set" parameters]]. Some parameters defined using the "set" command are associated to the app/applet and hence maintained when a new molecule is loaded, while others are reset when the model is removed. | ||
Latest revision as of 13:05, 11 July 2016
- 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:
- 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)
Contents
The Jmol Application and Applet have a command language that grew on the base of the command language of RasMol and its browser plugin MDL Chime. A set of commands is called a command script, and writing such sets of commands or scripts is called scripting. This is the major way of controlling the display of molecules in Jmol.
Documentation links
Documentation of Jmol's scripting language can be found here:
This is the official document. The style is encyclopedic, explaining each command in turn, as usual in reference manuals. In addition to this primary site, with latest updates, there are some mirror sites (see links at right).
An introduction to Jmol scripting is available here:
A more user-friendly, but less thorough, basic guide by Nathan Silva and David Marcey; part of the Online Macromolecular Museum at California Lutheran University.
Other
- Scripts can be included inside the molecular model file. See how to do it.
- Jmol scripting language has grown, among other features, by adding mathematical operators (JmolMath), control structures (loops, conditionals, etc.). You may be interested in this programming language approach.
Similar but different scripting languages
Chime's command language (see "About Chime" at http://molviz.org) is a superset of the command language of Roger Sayle's public domain application RasMol. (The command language of open-source RasMol has diverged somewhat from that in RasMol and Chime). The command language used by Jmol started with most of the Chime commands, but has outgrown it in a notable extent, allowing for many new capabilities.
*-RasMol (v≤2.6) | |----Chime Takes nearly all RasMol 2.6 commands and adds a few. | | | ----Jmol (v≥10) Takes many RasMol 2.6 and Chime 2.6 commands and adds a few. | | | ---Jmol (v≥11) Adds many new commands. | -----OpenRasMol (v≥2.7) Takes all RasMol 2.6 commands and adds a few.
RasMol commands not accepted by Jmol
These are some RasMol / OpenRasMol commands that are not accepted by Jmol (they will raise an error and will stop further execution of the script):
set cartoon ondefines that cartoon display should use arrowheads -- not needed in Jmol, since that is the default (and not changeable).set cartoon Ndefines the "depth" (i.e. thickness) of the ribbons; more or less similar to Jmol'scartoon N.color atom cpknew"cpkNew" is a color scheme for elements slightly diferent than the old default "cpk"; not available as such in Jmol. See Jmol Colors for a comparison.
Transversal documentation
Covering specific aspects or applications (not by command, and usually not exhaustive):
- Surfaces. Jmol can calculate and render surfaces around a molecule, or part of it, representing its "true" shape and volume. Moreover, isosurfaces, atomic and molecular orbitals, and mathematically defined surfaces can also be rendered. An introductory tutorial on creating macromolecular Jmol surfaces is available: An Introduction to Jmol Surface Displays, part of the Online Macromolecular Museum at California Lutheran University.
- Persistent and nonpersistent "set" parameters. Some parameters defined using the "set" command are associated to the app/applet and hence maintained when a new molecule is loaded, while others are reset when the model is removed.
