BioMolecular Explorer 3D: Frequently Asked Questions

Software for interactive molecular exploration in High School Biology courses.

 

BME3D Contents

Welcome
The Software and How to Install It
A Guide to These Resources
Explore the Molecules
Frequently Asked Questions
Contact Us/Credits

 
 
 

Frequently Asked Questions

 

Netscape:
Why would I want to install an ancient browser like Netscape 4.8?
What if I already have Netscape 4.8 installed on my computer?
What if I already have a different version of Netscape on my computer?

Chime:
What is MDL Chime?
What if I already have Chime installed?

Browser Information:
What are the incompatibilities with Netscape 7.2, Firefox, and Mozilla?
Why does Internet Explorer only work with some of the BME3D materials?

Other:
Are lesson plans available for these materials?
Where can I learn more about how to use Protein Explorer?
Where can I find more molecules to explore in 3D?
Where did the structures in BioMolecular Explorer 3D come from?
Your Questions

 

Why would I want to install an ancient browser like Netscape 4.8?
Netscape 4.8 has worked beautifully, and been thoroughly tested, with Chime for over 10 years. It is the most reliable, stable browser for all Chime resources. The addition of Netscape 7.2, Firefox and Mozilla to the stable of Chime compatible browsers is more than welcome, but since they are recent additions they simply have not been tested over time. We encourage you to try these more modern browsers- but it is always nice to have the tried and true backup, Netscape 4.8.

What if I already have Netscape 4.8 installed on my computer?
In that case, you do not need to install it again; just proceed to installation instruction #2, Chime Plug-in.

What if I already have a different version of Netscape on my computer?
It is important to pay attention to the version number: any version number beginning with "4.7" (for example, 4.75) will work just as well as 4.8. Versions earlier than 4.7 may not work; versions 5 and 6 will not work. You can have multiple versions of Netscape on your computer without causing any problems, so you do not need to uninstall another version in order to use version 4.8 or version 7.2.

What is MDL Chime?
MDL Chime is a free program that adds a specific functionality to certain browsers; namely, Chime adds the capability of interpreting 3D molecular data. The data are in the form of x, y, z coordinates, which dictate the position of every atom seen in the structure. Data files for thousands of molecular structures are freely available on the Internet at the Protein Data Bank, a searchable national database of biomolecular structures. For more information, see What is MDL Chime?

What if I already have Chime installed? Some of the resources, notably Protein Explorer, require the latest version of Chime.

  • To find out your version of Chime,
    • display the test page, right-click (Windows) or click and hold (Mac) on the pink ball, and from Chime's menu select "About..."
  • Windows: The latest version is Chime 2.6 SP6.
    • To uninstall your old version of Chime, use Start, Settings, Control Panel, Add/Remove programs. Then install the new version.
  • Mac: The latest version is Chime 2.6 SP3.
    • To uninstall your old version of Chime, go to the Applications (Classic or OS 9) folder, open the Netscape folder, then open the Plug-ins folder. In the Plug-ins folder, delete all three Chime files.

What are the incompatibilities with Netscape 7.2, Firefox, and Mozilla?
These three browsers appear to work pretty well with our resources, but we have only recently adapted our materials for them, so they are not as tried and true as Netscape 4.8 (which has worked with these materials for many years). The one known issue at this time (May 2005) is that in the Antibodies and Hemoglobin tutorials, the tutorial buttons that control font size do not work. This is an extremely minor incompatibility.

Why does Internet Explorer only work with some of the BME3D materials?
Internet Explorer (IE) does not support the type of communication between browser and plug-in that enables many Chime tutorials to work. This is a decision made by Microsoft. Protein Explorer and some tutorials have been adapted specifically to work with IE, and these are noted in the table of molecules on the Explore the Molecules page.

Are lesson plans available for these materials?
Very few lesson plans are currently available (Fall 2004). They are noted and linked next to the name of the resource when they are available. We provide general instructions for creating a lesson plan and 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 willing to share with other teachers, you can send it to us so we can review it and provide access for teachers.

Where can I learn more about how to use Protein Explorer?
To learn how to use Protein Explorer more fully, view the Protein Explorer Demo Movies, which introduce you to Protein Explorer step-by-step.

Where can I find more molecules to explore in 3D?
The MolviZ.org web site and the the World Index of Molecular Visualization have descriptions and links to many 3D tutorials, as well as other resources. The national databank of macromolecular structures is available at the Protein Data Bank web site.

Where did the structures in BioMolecular Explorer 3D come from?
Most of the structures are freely available through the Protein Data Bank (PDB), which archives all published empirical macromolecular 3D structure data. Some of the DNA data at BME3D are theoretical models, while other DNA data and all of the protein data are research results from X-ray crystallography. Each structure data file is identified with a 4-character PDB identification code. In Protein Explorer, these codes are the first four characters after "FirstView:" (at the top of the FirstView control panel), and are also displayed in the External Resources panel, accessed through the PE Site Map. External Resources also provides a link to the original source data at the PDB. The PDB identification codes are also usually mentioned in Guided Tutorials and Animations. In some cases (hemoglobin, lactase), a single polypeptide chain was extracted for a close-up view (see Fewer or Single Chains in External Rexources). In other cases (hemoglobin), additional chains were added with symmetry operations to complete the functional molecule (see Probable Quaternary Structures in External Resources). In several cases (hemoglobin, HIV protease, lactase, myosin) information about functional sites was added to the published PDB files to enable easy display in Protein Explorer's Features of the Molecule control panel.

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