Jmol/Index

This is an index page pointing to resources about Jmol and JSmol.

TerminologyTerminology

Jmol and JSmol mean pretty much the same thing. Jmol is the original name of the software, meaning "Java molecular". After a version was developed that does not require Java (it runs in web browsers' HTML5/Javascript) the name JSmol was added, meaning "JavaScript molecular".

Resources About JmolResources About Jmol

Resources About Jmol in ProteopediaResources About Jmol in Proteopedia

IntroductionsIntroductions

• Introduction to Jmol, a brief, non-technical page.
• Jmol, a longer, semi-technical page.
• FirstGlance in Jmol makes the power of Jmol accessible, without learning any command language. Essentially it provides guided exploration of any macromolecule. FirstGlance enables the user to concentrate on the molecule instead of how to use Jmol.

TechnicalTechnical

JSmol in ProteopediaJSmol in Proteopedia

• How JSmol Works
• Help:Making animations for Powerpoint: How to save a state-script from JSmol in any Proteopedia scene, drop it into FirstGlance and save a Powerpoint-slide-ready animation.
• Morphs explains how to animate transitions between two conformations of a macromolecule, and has links to many examples.
• Superposition with jmol: How to superimpose two structures in Jmol and show them in Proteopedia.
• Jmol/Visualizing membrane position for integral membrane proteins.
• User:James D Watson/Using Jmol for the more technically minded. A guide to using Jmol's menu. Compared to using FirstGlance in Jmol, this is slow and cumbersome, and the Jmol menu lacks any help or explanation.
• Jmol/Synchronization
• Jmol/Visualizing large molecules
• Electron density maps has links to methods and examples for showing electron density isomeshes in Proteopedia.
• JSmol/Rotation Speeds for models of various sizes and in different web browsers.

Using Jmol with JavaUsing Jmol with Java

• Distinguishing the modes of Jmol on Proteopedia: How to tell if Jmol is using Java or not.
• Installing and enabling Java
• Using Java for Rendering Structures: How to force Proteopedia to use the faster Jmol_S signed Java applet instead of its default, which is the slower JSmol.
• Jmol/Application: How to use the stand-alone Java application, in contrast to Jmol within a web browser.

ConversionConversion

• User:Wayne Decatur/Converting Exported Proteopedia Pages from Jmol to JSmol
• User:Eric Martz/JSmol Notes includes speed comparisons for Jmol_S (Java applet) vs. JSmol and partial notes about converting web resources from Jmol_S to JSmol.

History of JmolHistory of Jmol

• For a brief overview, see footnote 1 at Jmol.
• Detailed history at Sourceforge].

Resources About Jmol Outside of ProteopediaResources About Jmol Outside of Proteopedia

• Jmol.Org is the primary source for Jmol/JSmol downloads and its documentation. It includes
  • The Jmol Users EMail List is the best place to get technical help. Access it from the Jmol Projects Page at Sourceforge.
  • Default Color Schemes used by Jmol/JSmol.
• The Jmol Wiki has lots of information and help written and maintained by users, including notably
  • Hundreds of Websites that use Jmol.
• Jmol command script reference manual
• Bob Hanson's StOlaf.Edu online test site for current JSmol and Jmol_S.

See AlsoSee Also

• Introduction to molecular visualization
• Molecular modeling and visualization software
• Java
• Installing and enabling Java

RedirectsRedirects

There are redirects to this page from About Jmol, About JSmol, Help:Jmol and Help:JSmol.