#JMOL EXAMPLE USAGE SOFTWARE#
#JMOL EXAMPLE USAGE CODE#

cif (Crystalllographic Information Files) and c=0 for everything else. If these are not explicitly set, the filter defaults to controls appropriate for the structure file-type. ?c=3 to controls for display of biological macromolecules such as proteins or nucleic acids. ?c=2 to force crystallographic controls for display of unit cells, crystal packing and polyhedra for data fies that support these. ?c=1 to force 'default' controls for small inorganic or organic chemical structures. There is also a toggle button to display the viewer full-screen. Note that the end-user can also resize the viewer by mouse click-and-drag on the bottom-right corner. ?s=150 to set the viewer's size at 150 pixels.

Parameters can be added to the end of the URL to specify certain display options.

So default usage of the Jmol filter, for a structure water.pdb, in course 7 of .uk might use the code: The editor may 'scramble' things, particularly if you use additional parametes (below) and you may find it best to use HTML Source ( button) view.

use the Insert Web Link button and enter the URL of the resource (already uploaded into the course's Files folder).

use the Moodle text editor (inside a course topic, label, HTML block, forum posting, quiz question etc) to add the text for a link, eg 'water'.

Simply create a link to the molecule file, wherever you want the molecule viewer to appear.

(This is important - Jmol refuses to display data files held on other servers, so you can't just link to a file that exists somewhere else on the web.)

Upload a molecule data file to the Moodle server.

in a Label, a Forum discussion, or a Quiz question. The Jmol filter is very useful for including a molecule viewer in a variety of situations - e.g. Recent versions of the filter also have a Performance menu to adjust the rendering quality and improve performance on more limited client systems, mobiles etc. JSmol (the default) offers the widest cross-platform support though, for very large chemical structures, Jmol or GLmol offer faster performance. The Jmol filter provides the end-user with menu options to switch between JSmol (JavaScript), Jmol (Java) and GLmol (WebGL). This has good performance on hardware/software that supports WebGL but currently does not support all the features of JSmol. There is also an experimental WebGL version of Jmol, known as GLmol. Where the Java applet is required, recent versions of the filter use the self-signed applet, to minimise the security warnings/blocks generated by recent Java releases. That said, most recent browser versions now support binary file-handling by JavaScript. pdb.zip) are used with browsers that don't fully support binary file-handling by JavaScript, the Jmol Java applet is also used. Also, if certain chemical structure file-types (e.g.pse or.

If Internet Explorer 8 is used, the filter switches to the Jmol Java applet. In most circumstances, the Jmol filter defaults to using JSmol, the JavaScript/HTML5 version, for maximum cross-platform compatability. Note that JSmol is not a different program to Jmol: it is Jmol, just compiled into JavaScript instead of Java (thanks to the Java2Script software).

#JMOL EXAMPLE USAGE CODE#

JSmol allows rendering, scripting and interaction with the models just as Jmol does, since the source code is shared by both. No hardware-based graphics acceleration is used, allowing JSmol to run in any web browser that supports HTML5 standards. JSmol opens up the use of Jmol in PC, Mac, and Linux systems without Java installed or with Java disabled, as well as tablets and smart phones (both iOS and Android). Microsoft Edge and Google Chrome no longer support Java and support is being phased out for Safari, Opera and Firefox.Īs a result, the Jmol developers have created JSmol, an HTML5 canvas version of the Jmol applet that uses JavaScript. Unfortunately, more recent Java applet support by browsers has suffered from security and functionality issues. Originally, Jmol was a developed as a Java applet, requiring no additional capability on your Web server, but requiring both Java and a JavaScript-enabled browser for the user. The Moodle Jmol filter makes it incredibly simple for teachers to embed these viewers into teaching material (quizzes, discussion messages, etc). It can easily be embedded into a webpage.

#JMOL EXAMPLE USAGE SOFTWARE#

Jmol (Jsmol) is open-source software for interactive 3D viewing of chemical structures.

Jmol example usage