Jmol/Index: Difference between revisions

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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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 ==Terminology==
-''Jmol'' and ''JSmol'' mean pretty much the same thing. '''Jmol''' is the original name of the software, meaning &quot;'''J'''ava '''mol'''ecular&quot;. After a version was developed that does not require Java (it runs in web browsers' HTML5/Javascript) the name '''JSmol''' was added, meaning &quot;'''J'''ava'''S'''cript '''mol'''ecular&quot;.
+''Jmol'' and ''JSmol'' mean pretty much the same thing. '''Jmol''' is the original name of the software, meaning &quot;'''J'''ava '''mol'''ecular&quot;. After a version was developed that does not require Java (it runs in web browsers' HTML5/Javascript) the name '''JSmol'''<ref>DOI: 10.1002/ijch.201300024</ref> was added, meaning &quot;'''J'''ava'''S'''cript '''mol'''ecular&quot;.
 ==Resources About Jmol==
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 =====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.
-*[[Superposition with jmol]]: How to superimpose two structures in Jmol and show them in Proteopedia.
+*[[Electron density maps]] has links to methods and examples for showing electron density isomeshes in Proteopedia.
-*[[Jmol/Visualizing membrane position]] for integral membrane proteins.
+*[[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]]
-*[[Electron density maps]] has links to methods and examples for showing electron density isomeshes in Proteopedia.
+*[[Jmol/Visualizing membrane position]] for integral membrane proteins.
-*[[JSmol/Rotation Speeds]] for models of various sizes and in different web browsers.
 =====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]]
+*[[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.
-*[[Jmol/Application]]: How to use the stand-alone Java application, in contrast to Jmol within a web browser.
 =====Conversion=====
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 *[[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====
+===History of Jmol===
 *For a brief overview, see [[Jmol#cite_note-0|footnote 1 at Jmol]].
 *[http://jmol.sourceforge.net/history/ Detailed history at Sourceforge]].
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 *[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].
+**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/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==
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 ==Redirects==
 There are redirects to this page from [[About Jmol]], [[About JSmol]], [[Help:Jmol]] and [[Help:JSmol]].
+== References ==
+<references/>