Jmol: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Wayne Decatur, Jaime Prilusky, Angel Herraez, Joel L. Sussman

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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]] and [[How JSmol Works]]. An overview of other Jmol resources is at [[Jmol/Index]].		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'''"<ref>https://onlinelibrary.wiley.com/doi/10.1002/ijch.201300024 JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia</ref> 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]] and [[How JSmol Works]]. An overview of other Jmol resources is at [[Jmol/Index]].

	'''JSmol''' has proven quite satisfactory for interactive displays of most macromolecules in Proteopedia, and is the default. This avoids the need for Protepedia users to [[Installing_and_enabling_Java\|install and enable Java]]. 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]]).		'''JSmol''' has proven quite satisfactory for interactive displays of most macromolecules in Proteopedia, and is the default. This avoids the need for Protepedia users to [[Installing_and_enabling_Java\|install and enable Java]]. 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]]).