BioMolecular Explorer 3D: Frequently Asked Questions

Software for interactive molecular exploration in High School Biology courses.

   
 
 

Frequently Asked Questions

 

Teaching-related:
Are lesson plans available for these materials?
Can I get a copy of this web site on a CD?
Where can I find more molecules to explore in 3D?
Where did the structures in BioMolecular Explorer 3D come from?
Why don't you include RNA structure?
Your questions

General:
What is Jmol?
What's new in BME3D version 2.1?
What's new in BME3D version 2?

Troubleshooting & Technical:
Why can't I see the molecule?
Why don't the controls work?
What web browsers can I use to view the molecules?


 

Are lesson plans available for these materials?
Very few lesson plans are currently available (Oct 2007). They are noted and linked next to the name of the resource when they are available. We provide links to materials for each molecule that we hope will be helpful in preparing a lesson plan. If you create a lesson plan that you are would like our feedback on, send it to us: we will review it and get back to you.

Can I get a copy of this web site on a CD?
Version 2 is not yet available on CD, but we are developing it. For a copy of version 1, visit the 3dMolecularDesigns webite to purchase a CD. You may make copies of the CD freely for colleagues for educational uses!

Where can I find more molecules to explore in 3D?
Other websites that use Jmol are listed at the Jmol wiki. For tutorials that use require additional (free) software see the MolviZ.org web site and the the World Index of Molecular Visualization, which have descriptions and links to many 3D tutorials as well as other resources. The international databank of macromolecular structures is available at the Protein Data Bank (PDB) web site.

Where did the structures in BioMolecular Explorer 3D come from?
Most of the structures are freely available in the form of data files through the Protein Data Bank, which archives all published empirical macromolecular 3D structure data. Some of the DNA and lipid structures at BME3D are theoretical models, while other DNA structures and all of the protein structures are research results from X-ray crystallography. Each structure data file can be identified using its 4-character PDB identification code. PDB ID codes are displayed in the left-hand column of the page in FirstGlance in Jmol, and are often available in Jmol at the top line of the Jmol pop-up menu.

Why don't you include RNA structure?
We would like to, but as yet there are no overviews of RNA in Jmol of which we are aware. RNAs are an eclectic bunch, and we continue to look for a comprehensive resource. If you are aware of a Jmol version of RNA, please contact us with the URL.

Your Questions
Please contact us to ask any other questions about BioMolecular Explorer 3D software or the molecules.

What is Jmol?
Jmol is a small, free program that tells your your computer how to display molecules in 3d. The Jmol applet is a version of Jmol that works in a web page. The Jmol applet downloads with the web page itself, which is why the first molecule you view takes a little longer to appear than subsequent molecules. When you exit (quit) the browser, the browser discards the applet program, so it is no longer on your computer. The next time you visit a web page that uses Jmol, it downloads again. For more information on Jmol, visit the Jmol project home page.

What's new in version 2.1?
      • Hemoglobin Guided Tutorial returns! The Guided Tutorial of hemoglobin, originally part of BME3D v1, has been updated for inclusion in BME3D v2.1.

What's new in version 2?
      • No software or installation required! Software download and installation are no longer required for BME3d (version 2). BME3D version 1 required Chime, a free plug-in for browsers that must be downloaded and installed on your computer. Version 2 uses Jmol, a small program that downloads as a part of the web page, so you do not even have to know about it. Jmol only stays on your computer until you exit your browser.
      • Use any popular, modern browser! Because BME3D version 1 relied on Chime software to present molecules in 3d, some resources required an outdated browser, Netscape 4. Now that BME3D uses Jmol, all resources work in modern browsers. (More information).
      • No distinction between Mac and PC materials! All BME3D v2 resources work on both Mac and PC, and on linux!
      • New! Overviews of protein structure, lipids, carbohydrates, and vitamins! In addition to DNA, BME3D v2 now gives you access to 3d examples from these classes of molecules.
      • Note: Some Chime Tutorials are not included (yet). Some of the Chime Tutorials available in BME3D version 1 have not yet been adapted for Jmol, and remain available only at the BME3D version 1 web site. These tutorials are: Exploring DNA and Antibodies. We hope to adapt these for Jmol in the future.

Why can't I see the molecule?
The first time you view a molecule it may take a minute or more to appear - subsequent views will be much faster. The delay is caused by the downloading of the Jmol java applet, which displays the molecular structure in the web page. Once it downloads, it remains available for viewing subsequent molecules. In addition, time is required for the molecular structure file to reach your computer over the internet.

If you have waited 2 or 3 minutes and do not see the molecule, check that you are using a recommended browser. If you have tried to refresh or reload the web page while waiting, try simply quitting and re-starting the browser.

Java is required for Jmol. Almost all computers come with java installed. However, some installations of Windows or linux may have no java. You can install or update java (free) by going to java.com. Updating java is always a good idea, especially if Jmol does not seem to be working properly.

Why don't the controls work?
In the Safari browser on Mac 10.2 or 10.3, sometimes the links and buttons that control the molecular view fail to work. Simply quit and restart Safari to cure this problem, or upgrade to OSX 10.4 Tiger to avoid this problem entirely. If you are using another browser and encounter difficulties, try quitting and re-starting the browser. If that does not work, you may need to update the version of java on your computer. You can install or update java (free) by going to java.com. Updating java is always a good idea, especially if Jmol does not seem to be working properly.

What web browsers can I use to view the molecules?
Recommended browsers are the current versions of:

Windows (get/update java from java.com)

  • Internet Explorer
  • Netscape 7 or 8
  • Firefox
  • Mozilla

Mac OSX (Apple Software Upgrades include java. Keeping your software upgrades up to date is recommended.)

  • Safari 2
  • Firefox 1.5 (or later)

linux

  • Mozilla Firefox