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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/Quaternions]]: How to store and recall an orientation, and how to do fancy rotations.
*[[Jmol/Surfaces]]
*[[Jmol/Interactivity]]: Adding buttons etc. to the Proteopedia text to allow readers to modify the 3D scene.
*[[Jmol/Visualizing membrane position]] for integral membrane proteins.
*[[Jmol/Synchronization]]
*[[Jmol/Synchronization]]
*[[Jmol/Visualizing large molecules]]
*[[Jmol/Visualizing large molecules]]
*[[Jmol/Cavities pockets and tunnels]]
*[[Jmol/Visualizing membrane position]] for integral membrane proteins.
*[[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.
*[[JSmol/Rotation Speeds]] for models of various sizes and in different web browsers.
*[[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.


=====Using Jmol with Java=====
=====Using Jmol with Java=====
*[[Distinguishing the modes of Jmol on Proteopedia]]: How to tell if Jmol is using Java or not.
*[[Distinguishing the modes of Jmol on Proteopedia]]: How to tell if Jmol is using Java or not.
*[[Installing and enabling Java]]
*[[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]]
*[[PACUPP|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.
*[[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.


=====Conversion=====
=====Conversion=====
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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 online test site for current JSmol and Jmol_S].
*[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==

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

Eric Martz, Joel L. Sussman, Karsten Theis, Angel Herraez
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