World Wide Web Tools

Advanced Biochemistry Fall Term, 1997


Some of the links from these pages (or links from these links,etc.) will require that you set certain preferences in Netscape for optimal viewing. The most important are those that allow you to view molecular structures using the Chime plug-in or the RasMac and MAGE programs. (If you do not have them, the Chime plug-in and the RasMac and MAGE programs can be downloaded to your computer from their original sources.)
See below for setting up the Chime plug-in and setting other Netscape Appearance and Mail preferences.

To set up Netscape 3.01 for RasMac (or MAGE) viewing on any Mac, follow this sequence of steps:

  1. Select General Preferences... under the Netscape Options menu.
  2. Choose Helpers from the choices at the top.
  3. Scroll through the list to see if RasMac v2.6 is listed under Handled By.
  4. If not, click on the New... button.
  5. Enter "chemical/x-pdb" in the "Description" box; tab to the "MIME Type" box, and enter "chemical/x-pdb"; tab to the "Suffixes" box, and enter "pdb".
  6. Under Handled By, click on Application.
  7. Click on Browse... and open the copy of RasMac v2.6 on your machine.
  8. If all went well, your Helpers box should look like the highlighted line in the window shown below.
  9. Click on Apply; and then OK to close the Helper window. Netscape 3.0 will use the new Helper without having to be restarted.

A similar procedure is used for any other Helper you want to use with Netscape. For example, the applications MAGE, Microsoft Word, and Microsoft Excel are set up by doing steps 4-7 above, and entering the following items in the indicated boxes:
ApplicationDescriptionMIME TypeSuffixes
RasMacchemical/x-pdbchemical/x-pdbpdb
MAGEchemical/x-kinemagechemical/x-kinemagekin
MS Wordapplication/mswordapplication/mswordWORD
MS Excelapplication/excelapplication/excelXL
If Netscape is set up properly to use RasMac 2.6 and MAGE_4.0 from these pages, your Helpers window will be similar to the one pictured above. If not, use this page to make changes or contact W. McClure.

Chemscape Chime v1.0 is a Netscape plug-in that allows you to view and manipulate molecular models on WWW pages. The CMU Cluster Macs and Windows machines have Chime installed in the Netscape plug-ins folder. To see whether it is installed on your Mac, select "About Plugins..." under the menu while you are in Netscape.
If your Mac is not in a cluster, see the downloading intructions for details on the installation of this plug-in, and follow the on-screen instructions for putting it into your Netscape 3.01 plug-in folder.
After you have installed Chime, you should look at the CMU Chime Features page, for a short demonstration on how this plug-in is used.
Some notes on this and other plug-ins on any Mac computer:

Additional Netscape Options to consider:

  1. In the General Preferences window, there are two categories to select:
    • Use any Font and Colors you prefer. Netscape documents are "text only", so you decide how to view them. However, since some of the course material uses special symbols (such as -helix, -sheet, etc. ) that are not affected by font type and size, you may want to choose a combination that keeps these characters in line.
    • Under Appearance, changing Show Toolbar As to "text" will make more space on your Netscape page. In addition, the Toolbar, Location, and Directory Buttons can all be removed from the top of your page by deselecting them under Options. (And if you haven't already turned off the underlining of links, try it. These pages (and everything else on the WWW) look much cleaner without that default Netscape feature.)
  2. To send mail from a WWW page, choose Mail and News Preferences... under the Netscape Options menu and then select Servers. Enter "smtp.andrew.cmu.edu" in the Outgoing Mail (SMTP) Server: box; enter "@andrew.cmu.edu" in the Incoming Mail (POP) Server: box; enter your user ID in the last box; and fill in the other items with your preferences.

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Last modified August 29, 1997