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
What if I already have Chime installed?
Some of the resources, notably Protein Explorer, require the latest version
- 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
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
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.
Please contact us to ask any other questions
about BioMolecular Explorer 3D software or the molecules.