Jmol: Difference between revisions

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]] and [[How JSmol Works]].

'''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]]).  

Performance of JSmol [[User:Eric_Martz/JSmol_Notes#Poor_performance_in_Internet_Explorer.2C_Edge.2C_Chrome_and_Opera|varies with the web browser employed]]. In early 2017, '''Firefox''' gives smoothest rotation in JSmol. Rotation is jerkier in Chrome and Safari. Poorest performance occurs with Internet Explorer and Edge, which are therfore not recommended when using Proteopedia.

 

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]].

==Jmol Has Four Forms==

Proteopedia, [[FirstGlance in Jmol]],

<font color="red"><b>Jmol_S</b></font> (in web browser)

Yes: signed applet

Optional: see [[Using_Java_for_Rendering_Structures#Java-mode:_setting_a_preference_to_use_Jmol_S_.28Java.29_automatically_for_rendering_structures_in_Proteopedia|Preferences in Proteopedia]] (requires account/login) and at [http://firstglance.jmol.org FirstGlance in Jmol]. Proteopedia will use [[Using_Java_for_Rendering_Structures|Java on a page by page basis]] when "?use=java" is added at the end of the address (URL).

 

Older legacy websites that have not been updated:

in 2014, most at [http://molviz.org MolviZ.Org] and

[http://biomodel.uah.es/en/model1/ Biomodel-1].

 

All four forms of Jmol can be downloaded in a single package from [http://jmol.org Jmol.Org].

*January 26, 2014: Proteopedia upgraded to using a version of Jmol (version 14.0.7) that allows two modes. Proteopedia defaults to run Jmol in an HTML5/Javascript-mode not requiring [[Java]], but users can optionally use Jmol running as a signed Java applet. See [[Using Java for Rendering Structures|here]] for how to opt in to Java mode.