Jmol/Index: Difference between revisions
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*[[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. | *[[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. | *[[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/superposition]]: How to superimpose two structures in Jmol and show them in Proteopedia. | ||
*[[Jmol/ | *[[Jmol/Surfaces]] | ||
*[[Jmol/Synchronization]] | *[[Jmol/Synchronization]] | ||
*[[Jmol/Visualizing large molecules]] | *[[Jmol/Visualizing large molecules]] | ||
*[[Jmol/ | *[[Jmol/Visualizing membrane position]] for integral membrane proteins. | ||
=====Using Jmol with Java===== | =====Using Jmol with Java===== | ||
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*[http://wiki.jmol.org The Jmol Wiki] has lots of information and help written and maintained by users, including notably | *[http://wiki.jmol.org The Jmol Wiki] has lots of information and help written and maintained by users, including notably | ||
**Hundreds of [http://wiki.jmol.org/index.php/Websites_Using_Jmol Websites that use Jmol]. | **Hundreds of [http://wiki.jmol.org/index.php/Websites_Using_Jmol Websites that use Jmol]. | ||
**A list of [http://wiki.jmol.org/index.php/Literature published articles and books that describe Jmol features or uses]. | |||
*[https://chemapps.stolaf.edu/jmol/docs/ Jmol command script reference manual] | *[https://chemapps.stolaf.edu/jmol/docs/ Jmol command script reference manual] | ||
*[https://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm Bob Hanson's StOlaf.Edu | *[https://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm Bob Hanson's StOlaf.Edu site demonstrating current JSmol and Jmol signed Java applet]. | ||
==See Also== | ==See Also== | ||