Jmol: Difference between revisions

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Jmol<ref>Jmol was initiated before 2000 by [http://openscience.org 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, [http://www.stolaf.edu/people/hansonr/ Robert M. Hanson] became lead developer, and has vastly enhanced Jmol's capabilities. For more, see [http://jmol.sourceforge.net/history/ History of Jmol Development].</ref><ref>Biomolecules in the computer: Jmol to the rescue. Angel Herráez,[http://www3.interscience.wiley.com/journal/113449000/abstract ''Biochem. Mol. Biol. Ed.'' '''34''':255-61, 2006].</ref><ref name="jmolparadigmshift" /><ref>[http://wiki.jmol.org:81/index.php/Literature Jmol Literature] at the Jmol.Org wiki.</ref> is a free, open-source [[Molecular modeling and visualization software|molecular visualization]] software package. It is the primary visualization software used in Proteopedia. Jmol is a [http://en.wikipedia.org/wiki/Cross-platform cross-platform] program written in [[Java]], but able to run in an ~~HTML~~/Javascript-mode that does not require [[Java]]. [[Java]], particularly in web browsers, may be a [[Java#Java is a security threat|security risk]], and some [[Java#How to be as safe as possible with Java|simple precautions are recommended]].

Jmol<ref>Jmol was initiated before 2000 by [http://openscience.org 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, [http://www.stolaf.edu/people/hansonr/ Robert M. Hanson] became lead developer, and has vastly enhanced Jmol's capabilities. For more, see [http://jmol.sourceforge.net/history/ History of Jmol Development].</ref><ref>Biomolecules in the computer: Jmol to the rescue. Angel Herráez,[http://www3.interscience.wiley.com/journal/113449000/abstract ''Biochem. Mol. Biol. Ed.'' '''34''':255-61, 2006].</ref><ref name="jmolparadigmshift" /><ref>[http://wiki.jmol.org:81/index.php/Literature Jmol Literature] at the Jmol.Org wiki.</ref> is a free, open-source [[Molecular modeling and visualization software|molecular visualization]] software package. It is the primary visualization software used in Proteopedia. Jmol is a [http://en.wikipedia.org/wiki/Cross-platform cross-platform] program written in [[Java]], but able to run in an HTML5/Javascript-mode called "JSmol" that does not require [[Java]]. Jmol is also available as a stand-alone [[Jmol/Application|application]]. See [[#Jmol Has Four Forms|4 forms of Jmol]].

Jmol is available either as a ~~stand-alone [[Jmol/Application|application]]~~, or as a web browser applet.

[[Java]], particularly in web browsers, may be a [[Java#Java is a security threat|security risk]], and some [[Java#How to be as safe as possible with Java|simple precautions are recommended]].

Jmol is available either as a , or as a web browser applet.

'''At this time, Jmol still performs best in Java mode and users are encouraged to use that on Proteoepdia.''' See [[Using Java for Rendering Structures|here]] for how to opt in to Java mode.

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-Jmol<ref>Jmol was initiated before 2000 by [http://openscience.org 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, [http://www.stolaf.edu/people/hansonr/ Robert M. Hanson] became lead developer, and has vastly enhanced Jmol's capabilities. For more, see [http://jmol.sourceforge.net/history/ History of Jmol Development].</ref><ref>Biomolecules in the computer: Jmol to the rescue. Angel Herráez,[http://www3.interscience.wiley.com/journal/113449000/abstract  ''Biochem. Mol. Biol. Ed.'' '''34''':255-61, 2006].</ref><ref name="jmolparadigmshift" /><ref>[http://wiki.jmol.org:81/index.php/Literature Jmol Literature] at the Jmol.Org wiki.</ref> is a free, open-source [[Molecular modeling and visualization software|molecular visualization]] software package. It is the primary visualization software used in Proteopedia. Jmol is a [http://en.wikipedia.org/wiki/Cross-platform cross-platform] program written in [[Java]], but able to run in an HTML/Javascript-mode that does not require [[Java]]. [[Java]], particularly in web browsers, may be a [[Java#Java is a security threat|security risk]], and some [[Java#How to be as safe as possible with Java|simple precautions are recommended]].
+Jmol<ref>Jmol was initiated before 2000 by [http://openscience.org 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, [http://www.stolaf.edu/people/hansonr/ Robert M. Hanson] became lead developer, and has vastly enhanced Jmol's capabilities. For more, see [http://jmol.sourceforge.net/history/ History of Jmol Development].</ref><ref>Biomolecules in the computer: Jmol to the rescue. Angel Herráez,[http://www3.interscience.wiley.com/journal/113449000/abstract  ''Biochem. Mol. Biol. Ed.'' '''34''':255-61, 2006].</ref><ref name="jmolparadigmshift" /><ref>[http://wiki.jmol.org:81/index.php/Literature Jmol Literature] at the Jmol.Org wiki.</ref> is a free, open-source [[Molecular modeling and visualization software|molecular visualization]] software package. It is the primary visualization software used in Proteopedia. Jmol is a [http://en.wikipedia.org/wiki/Cross-platform cross-platform] program written in [[Java]], but able to run in an HTML5/Javascript-mode called &quot;JSmol&quot; that does not require [[Java]]. Jmol is also available as a stand-alone [[Jmol/Application|application]]. See [[#Jmol Has Four Forms|4 forms of Jmol]].
-Jmol is available either as a stand-alone [[Jmol/Application|application]], or as a web browser applet.
+[[Java]], particularly in web browsers, may be a [[Java#Java is a security threat|security risk]], and some [[Java#How to be as safe as possible with Java|simple precautions are recommended]].
+Jmol is available either as a , or as a web browser applet.
 '''At this time, Jmol still performs best in Java mode and users are encouraged to use that on Proteoepdia.''' See [[Using Java for Rendering Structures|here]] for how to opt in to Java mode.