FAQ

Table of Contents: Which Web browsers can run COMBOSA3D? COMBOSA3D has been tested with the Chime 2.0 plugin in Internet Explorer 5.0 and 5.5 (Windows), Netscape Communicator 4.6 (Windows), and Netscape Communicator 4.6 (Mac). It has been tested without the Chime 2.0 plugin in Internet Explorer 4.5 (Mac) and Netscape Communicator 4.6 (Linux). Apparently, Chime is not supported by new versions of Internet Explorer, beginning with service pack 2 for version 5.5.

How do I recover from a plugin error when using COMBOSA3D in Internet Explorer? Occasionally, Internet Explorer generates a "plugin error" message when the Chime plugin is used. If a plugin error occurs you can fix the problem by exiting and then relaunching Internet Explorer. A setting in Internet Explorer 5.0 can cause Chime to fail. You can correct this problem as follows:

  • Choose Internet Options from the Tools menu.
  • Click the Advanced tab in the dialog box that opens.
  • Uncheck Launch browser windows in a separate process.
  • Click OK.
  • Exit Internet Explorer, then restart Internet Explorer.
How do I run COMBOSA3D scripts in RasMol? The method used to run scripts in RasMol will vary slightly depending on the operating system you are using. On Windows platforms, copy the script and paste it into a text editor. Save the script as a text file (so that it has the .txt extension), and place it into the same folder as RasMol. Load the molecule you wish to examine into RasMol, then type script followed by the name of your text file (include the .txt extension) into the RasMol Command Line window and press enter. For more information on using RasMol see the RasMol manual.

How can I take a screen shot of the output of COMBOSA3D? On most Windows platforms you can press ALT + PRINT SCREEN to copy a picture of the active window to the Clipboard. The contents of the Clipboard can then be pasted into a graphics program for editing, saving, and printing. On the Mac, pressing SHIFT + Apple + 3 will save a picture of the screen to a file named Picture1, Picture2, etc.

Why don't COMBOSA3D alignments print properly when colored backgrounds are used? HTML tables are used to add background coloring to letters when the colored backgrounds option is used. Some Internet Explorer versions have an option to allow colored backgrounds to be printed. For example, with Internet Explorer 5.5 (Windows) you can allow backgrounds to be printed by doing the following:

  • Choose Internet Options from the Tools menu.
  • Click the Advanced tab in the dialog box that opens.
  • Under the Printing category check Print background colors and images.
  • Click OK.
In many versions of Netscape Communicator you can print backgrounds as follows:
  • Choose Page Setup from the File menu.
  • In the Page Options section check Print backgrounds.
  • Click OK.
Another way to print alignments is to generate a PDF using Acrobat Distiller. This technique has been used on the Macintosh using Netscape Communicator 4.6 (thanks to Russell Reagan for this information):
  • Choose Page Setup from the File menu.
  • In the Page Options section check Print backgrounds.
  • Click OK.
  • Choose Print from the File menu.
  • Check Print to file in the Print dialog box.
  • Click OK.
  • Use Acrobat Distiller to convert the postscript file to a PDF.
  • The PDF can be modified using Adobe Illustrator. For example, you can add asterisks and bars to highlight portions of interest in the alignment.
The best way to print alignments if your browser does not print the colored backgrounds is to take a screen shot.

How do I save the reference alignment? If you are using Netscape select Save As from the File menu. Enter a file name and select HTML Files from the Save as type list and click Save (the procedure may differ slightly between Netscape versions). If you are using Internet Explorer select Save As from the File menu. Enter a file name and select Web Page HTML only from the Save as type list. Click Save to save the file (the procedure may differ slightly between Internet Explorer versions).