Molecular surfaces can be calculated by Jmol, but for large molecules this can be quite CPU intensive and time consuming to do on the fly. you may need to do this several times, depending on the script.įor a more comprehensive treatment, see the Jmol If you get an unresponsive script, please choose continue. This is especially true now that we are using JSmol and HTML5 instead of the java-based Jmol. Note: surfaces require a lot of memory and are slow to load. This helps with funding opportunities for the OMM and helps ensure continued development of this resource. And please drop an email to with a link to your page/s.
![jmol applet jmol applet](https://i6.apk.fun/org.openscience.jmolandroid+5QAHwn9vMB.png)
Note: if this tutorial is helpful in the creation of your own webpages, please explicitly acknowledge your use of this page (URL, Author, date accessed, and a link to this page) in your webpage/s. The slide show below shows the three steps for doing this click on any slide to advance to the next slide.Back to OMM Exhibits An Introduction to Jmol Surface Displays ** The third one, called "jmolApplet", embeds the Jmol image on the page it should be placed where you want the image to be located.įor the first script, open the page.html file, then open the section of the page, and drag-and-drop the script icon from the "Head" tab of the Object pallet into the section of the page. The second one, called "jmolInitialize", should be placed at the beginning of the section and tells the page where the JmollApplet files are located. The first one estabishishes a link to the "Jmol.js" script library. Three Javascripts are needed to embed a Jmol image into page1.html one in the section of the page, and the other two in the section.
JMOL APPLET DOWNLOAD
Download it an place it in the site directory: The pdb file for the 3-Isopropylmalate dehydrogenase (1A05.pdb) can be downloaded by clicking here. Use GoLive to add a new page to the site and name it "page1.html"Ī pdb file containing the coordinants of the molecule that will be viewed in the Jmol image, also needs to be added to the site. The image will be placed on page1.html, within the new site. Here are the steps that can be used to embed a Jmol image in a web page.
![jmol applet jmol applet](https://wiki.jmol.org/images/4/40/JmolApplication_12-0.png)
![jmol applet jmol applet](https://image2.slideserve.com/4139667/jmol-application-showing-jspecview-as-a-tool-ir-l.jpg)
Only seven of the files need to be included in the web site the seven numbered JmolApplet#.jar files.
JMOL APPLET SOFTWARE
The software is downloaded as gzipped tar file, which when expanded, comprises a folder containing the following files:
![jmol applet jmol applet](https://www.linuxjournal.com/sites/default/files/styles/360_250/public/nodeimage/story/12153jmolf2.png)
Version 10.00.43, which was used in creating this tutorial, can be downloaded by clicking here. The Jmol applet software is open source and the most recent version can be downloaded from the website.
JMOL APPLET CODE
For this to work, the Jmol applet code must be reside in the web site that serves pages containing Jmol images. The software required for a browser to view a Jmol image is downloaded to the browser when a web page containing Jmol image is loaded into the browser. There are no plugins that need to be installed for a browser to view a web page containing a Jmol image. Because Jmol is Java based, it does not require anything of the browser except that it be Java capable. It contains an initialization script which highlights and orients it to look like the image on. Setting Up a Site for Embedding Jmol Images:īelow is an embedded Jmol image.