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 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]].

[[~~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~~]].

JSmol has proven quite satisfactory for interactive displays of most macromolecules in Proteopedia. The Java applet Jmol [[User:Eric_Martz/JSmol_Notes#JSmol_is_slower_than_Jmol performs much faster]], but this enhanced performance is not needed unless the model contains >~30,000 atoms, or multiple larger models (see [[NMR]]).

~~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.~~

Should you wish to try the Java applet, see [[Using Java for Rendering Structures]]. [[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]].

~~The Jmol applet is also used~~ in [[~~Molecular Workbench~~]] and in [[#~~Use in Scientific Journals~~|~~scientific journals~~]].

For more information and downloads, please see [http://jmol.org Jmol.Org].

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@@ Line 1: / Line 1: @@
 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]].
-[[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]].
+JSmol has proven quite satisfactory for interactive displays of most macromolecules in Proteopedia. The Java applet Jmol [[User:Eric_Martz/JSmol_Notes#JSmol_is_slower_than_Jmol performs much faster]], but this enhanced performance is not needed unless the model contains >~30,000 atoms, or multiple larger models (see [[NMR]]).
-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.
+Should you wish to try the Java applet, see [[Using Java for Rendering Structures]]. [[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]].
-The Jmol applet is also used in [[Molecular Workbench]] and in [[#Use in Scientific Journals|scientific journals]].
 For more information and downloads, please see [http://jmol.org Jmol.Org].