Difference between revisions of "Jmol Applet"
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The '''unsigned''' applet displays the molecule without asking the user to trust it. However, it is limited (for security reasons) to loading molecular models from the same http domain (server) that downloads the applet itself. [http://firstglance.jmol.org/ FirstGlance in Jmol] uses the unsigned applet by default, but the signed applet will be used when that "Advanced Option" is checked. Thus you can easily see both applets in action. Methods for accessing data files from arbitrary servers are described in some detail at [http://bioinformatics.org/firstglance/fgij/datameth.htm PDB Data File Access Methods]. | The '''unsigned''' applet displays the molecule without asking the user to trust it. However, it is limited (for security reasons) to loading molecular models from the same http domain (server) that downloads the applet itself. [http://firstglance.jmol.org/ FirstGlance in Jmol] uses the unsigned applet by default, but the signed applet will be used when that "Advanced Option" is checked. Thus you can easily see both applets in action. Methods for accessing data files from arbitrary servers are described in some detail at [http://bioinformatics.org/firstglance/fgij/datameth.htm PDB Data File Access Methods]. | ||
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| + | ===Tools for Authoring Jmol Web Pages=== | ||
| + | If you are not comfortable writing html and javascript code or would just like to quickly put together some simple pages look at the program [http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/Jmol_Web_Page_Maker.shtml Jmol_Web_Page_Maker]. This is a java application that will generate simple interactive Jmol pages using a GUI interface where you can select the data files and and some basic parameters. I wrote version 1.0 of this program.--[[User:Gutow|Gutow]] 18:13, 18 July 2006 (CEST) | ||
Revision as of 16:13, 18 July 2006
Contents
Jmol Applet
Java applet version of Jmol which allows Jmol to be embedded in web pages (given that viewers have a Java plugin installed). Like with the application, Scripting is available. For some demonstration pages see http://www.jmol.org/demo/. To see the HTML source use your web browser View → Page Source.
Additionally, Jmol can also be installed locally, e.g. on the hard disk or on CD. See Jmol Applet Deployment Local.
Jmol in Wikis
The applet can be embedded in HTML (or XHTML) pages (examples are listed on Websites Using Jmol), but also, with some extra technologies, in Wiki pages (see Jmol Processor).
Unsigned vs. Signed Applet & Data Access
The signed applet can load a molecular model from any http or ftp URL. However, the user will be asked to trust the signed applet. This could be problematic since the publishing authority (jmol.org) "cannot be verified", and the security certificate was issued by a group that is "not trusted" (jmol.org). This is because it would be costly and cumbersome for each version of the applet to be signed by a trusted (commercial) authority.
The unsigned applet displays the molecule without asking the user to trust it. However, it is limited (for security reasons) to loading molecular models from the same http domain (server) that downloads the applet itself. FirstGlance in Jmol uses the unsigned applet by default, but the signed applet will be used when that "Advanced Option" is checked. Thus you can easily see both applets in action. Methods for accessing data files from arbitrary servers are described in some detail at PDB Data File Access Methods.
Tools for Authoring Jmol Web Pages
If you are not comfortable writing html and javascript code or would just like to quickly put together some simple pages look at the program Jmol_Web_Page_Maker. This is a java application that will generate simple interactive Jmol pages using a GUI interface where you can select the data files and and some basic parameters. I wrote version 1.0 of this program.--Gutow 18:13, 18 July 2006 (CEST)
Contributors
AngelHerraez, GregE, EricMartz, Hansonrstolaf, Igor, NicolasVervelle, Gutow, Ted, Pimpim, Cudo29, Green
