Jmol: Difference between revisions
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==Command Scripting Language== | ==Command Scripting Language== | ||
Jmol has an extensive and powerful command language<ref name="jmol-commands">Documentation for Jmol's command language is available from [http://jmol.org Jmol.Org]. An overview is at [http://jmol.sourceforge.net/docs/ jmol.org/docs], and additional coverage of specific topics is at the [http://wiki.jmol.org Jmol Wiki]. The command reference manual is at [http://chemapps.stolaf.edu/jmol/docs/ chemapps.stolaf.edu/jmol/docs/].</ref> that specifies molecular scenes. A molecular scene consists of the rendering or display for each part of the molecular model (e.g. ribbon cartoon, ball and stick, etc.), optionally hiding some parts of the model, the color or color scheme for each moiety, optional labels (attached to an atom) or signs (text in | Jmol has an extensive and powerful command language<ref name="jmol-commands">Documentation for Jmol's command language is available from [http://jmol.org Jmol.Org]. An overview is at [http://jmol.sourceforge.net/docs/ jmol.org/docs], and additional coverage of specific topics is at the [http://wiki.jmol.org Jmol Wiki]. The command reference manual is at [http://chemapps.stolaf.edu/jmol/docs/ chemapps.stolaf.edu/jmol/docs/].</ref> that specifies molecular scenes. A molecular scene consists of the rendering or display for each part of the molecular model (e.g. ribbon cartoon, ball and stick, etc.), optionally hiding some parts of the model, the color or color scheme for each moiety, optional labels (attached to an atom) or signs (text in fixed locations), and the orientation and zoom (magnification) of the molecule. Jmol's command language is a superset of the [[RasMol]] and [[Chime]] command languages. | ||
A '''command script''' or simply '''script''' is a series of commands recorded in a file. Script files are [[plain text]], and their filenames end with '''.spt'''. | A '''command script''' or simply '''script''' is a series of commands recorded in a file. Script files are [[plain text]], and their filenames end with '''.spt'''. | ||
Revision as of 00:39, 17 December 2009
Jmol[1][2][3] is a free, open-source molecular visualization software package. Its applet is the primary visualization software used in Proteopedia. Jmol is a cross-platform program written in java, and is available either as a stand-alone application, or as a web browser applet.
The Jmol applet is also used in Molecular Workbench.
For more information and downloads, please see Jmol.Org.
Command Scripting LanguageCommand Scripting Language
Jmol has an extensive and powerful command language[4] that specifies molecular scenes. A molecular scene consists of the rendering or display for each part of the molecular model (e.g. ribbon cartoon, ball and stick, etc.), optionally hiding some parts of the model, the color or color scheme for each moiety, optional labels (attached to an atom) or signs (text in fixed locations), and the orientation and zoom (magnification) of the molecule. Jmol's command language is a superset of the RasMol and Chime command languages.
A command script or simply script is a series of commands recorded in a file. Script files are plain text, and their filenames end with .spt.
Proteopedia's Scene Authoring Tools free Proteopedia users from the burden of learning Jmol's command language, by enabling them to author complex molecular scenes from menus, buttons, checkboxes and forms. Further, Proteopedia saves customized molecular scenes in the form of state scripts.
State ScriptsState Scripts
Jmol has the capability to generate a command script that will recreate whatever molecular scene it is currently displaying, including all details and the orientation of the molecule. Proteopedia uses this capability to save scenes created with its Scene Authoring Tools so they can be displayed in its web pages and thereby easily shared.
See AlsoSee Also
ReferencesReferences
- ↑ Jmol was initiated before 2000 by Dan Gezelter, and many programmers contributed to it including Bradley A. Smith, Egon Willighagen, and Cristoph Steinbeck. In 2002, Miguel Howard volunteered as the primary developer. He made many major enhancements including drastically improved performance, support for macromolecules, and implementation of the RasMol / Chime script command language. Howard's work culminated in the release of an open-source replacement for Chime in 2006. Subsequently, Robert M. Hanson became lead developer, and has vastly enhanced Jmol's capabilities. For more, see History of Jmol Development.
- ↑ Biomolecules in the computer: Jmol to the rescue. Angel Herráez,Biochem. Mol. Biol. Ed. 34:255-61, 2006.
- ↑ Jmol Literature at the Jmol.Org wiki.
- ↑ Documentation for Jmol's command language is available from Jmol.Org. An overview is at jmol.org/docs, and additional coverage of specific topics is at the Jmol Wiki. The command reference manual is at chemapps.stolaf.edu/jmol/docs/.