Jmol/Index

From Proteopedia

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

Terminology

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^[1] was added, meaning "JavaScript molecular".

Resources About Jmol

Resources About Jmol in Proteopedia

Introductions

• 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.

Technical

JSmol 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.
• Electron density maps has links to methods and examples for showing electron density isomeshes in Proteopedia.
• Help:Copying FirstGlance Scenes into Proteopedia: Some views are much easier to get in FirstGlance than in the SAT, and can easily become green links in Proteopedia.
• 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.

Alphabetically:

• Jmol/Cavities pockets and tunnels as isosurfaces.
• Jmol/debugging: How to debug Jmol scripts.
• Jmol/Depth from surface: How to color an isosurface (or atoms) by depth from the structure's surface.
• Jmol/Electrostatic potential
• Jmol/Interactivity: Adding buttons etc. to the Proteopedia text to allow readers to modify the 3D scene.
• Jmol/Quaternions: How to store and recall an orientation, and how to do fancy rotations.
• JSmol/Rotation Speeds for models of various sizes and in different web browsers.
• Jmol/State: Reverse engineering the Jmol state to get human-readable commands that generate the same scene.
• Jmol/superposition: How to superimpose two structures in Jmol and show them in Proteopedia.
• Jmol/Surfaces
• Jmol/Synchronization
• Jmol/Visualizing large molecules
• Jmol/Visualizing membrane position for integral membrane proteins.

Using Jmol with Java

• Distinguishing the modes of Jmol on Proteopedia: How to tell if Jmol is using Java or not.
• Installing and enabling Java
• Jmol/Application: How to use the stand-alone Java application, in contrast to Jmol within a web browser.
• Jmol/PDB file editing with Jmol
• Pockets And Cavities Using Pseudoatoms in Proteins (PACUPP), an application written entirely in Jmol command scripts.
• 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.

Conversion

• 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 Jmol

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

Resources 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.
  • A list of published articles and books that describe Jmol features or uses.
• Jmol command script reference manual
• Bob Hanson's StOlaf.Edu site demonstrating current JSmol and Jmol signed Java applet.

See Also

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

Redirects

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

References

1. ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024