Scripting - Revision history

AngelHerraez: RasMol commands not accepted by Jmol

2016-07-11T13:05:13Z

RasMol commands not accepted by Jmol

AngelHerraez: reinforce refs to scripting

2013-08-31T09:58:20Z

reinforce refs to scripting

AngelHerraez: /* Documentation links */ scripts inline the model

2009-06-14T11:58:47Z

‎Documentation links: scripts inline the model

AngelHerraez: use the ScriptingDoc template

2009-05-26T08:40:48Z

use the ScriptingDoc template

AngelHerraez: /* Documentation links */

2008-11-12T23:56:46Z

‎Documentation links

Marcey at 17:20, 5 January 2008

2008-01-05T17:20:58Z

Marcey: added a link to Jmol Surface Displays tutorial...for beginners.

2008-01-05T17:18:39Z

added a link to Jmol Surface Displays tutorial...for beginners.

NicolasVervelle: Reverted edits by XplJid (Talk); changed back to last version by Pimpim

2007-07-14T18:44:18Z

Reverted edits by XplJid (Talk); changed back to last version by Pimpim

Anonymous at 17:00, 14 July 2007

2007-07-14T17:00:10Z

Pimpim: belongs to different template now

2007-06-27T17:09:53Z

belongs to different template now

@@ Line 1: / Line 1: @@
 {{Jmol_Documentation_Sections}}
 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.
@@ Line 32: / Line 33: @@
     -----OpenRasMol (v&ge;2.7)   Takes all RasMol 2.6 commands and adds a few.
 </pre>
 = Transversal documentation =

@@ Line 1: / Line 1: @@
 {{Jmol_Documentation_Sections}}
-The Jmol [[Jmol_Application|Application]] and [[Jmol_Applet|Applet]] have a command language that grows on the base of [http://www.mdl.com/support/developer/chime/developer_tools.jsp command language] of the 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''.
+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 =
@@ Line 16: / Line 16: @@
 '''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]].
 = Similar but different scripting languages =

@@ Line 13: / Line 13: @@
 * 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.
 = Similar but different scripting languages =

@@ Line 6: / Line 6: @@
 '''Documentation of Jmol's scripting language can be found here:'''
-* http://www.stolaf.edu/academics/chemapps/jmol/
+* {{ScriptingDoc}}
 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).

@@ Line 8: / Line 8: @@
 * http://www.stolaf.edu/academics/chemapps/jmol/
 This is the official document. The style is encyclopedic, explaining each command in turn, as usual in reference manuals.
 '''An introduction to Jmol scripting is available here:'''

@@ Line 30: / Line 30: @@
 = 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.
+* [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.

@@ Line 17: / Line 17: @@
 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>
-*-RasMol (v
+*-RasMol (v&le;2.6)

← Older revision		Revision as of 17:09, 27 June 2007
Line 1:		Line 1:
−	{{~~Tutorials_Sections~~}}	+	{{Jmol_Documentation_Sections}}

	The Jmol [[Jmol_Application\|Application]] and [[Jmol_Applet\|Applet]] have a command language that grows on the base of [http://www.mdl.com/support/developer/chime/developer_tools.jsp command language] of the 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''.		The Jmol [[Jmol_Application\|Application]] and [[Jmol_Applet\|Applet]] have a command language that grows on the base of [http://www.mdl.com/support/developer/chime/developer_tools.jsp command language] of the 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''.