1. All files and folders inside "PyMoodMainDir" (on Windows and Linux) or inside the folder "PyMood" (on Mac) should be named without any spaces. If you need to include a space between words in the file name, use the symbol _ (underscore). For example: R_norvegicus_library_1.fasta

2. On Windows 2000/XP, you are strongly recommended to have file extensions visible in the Windows file viewer. PyMood may be difficult to use without them. To enable them (or make sure they are enabled) follow these instructions:
  1. Open My Computer
  2. Click on the Tools menu, and then select Folder Options...
  3. In the new window, click on the View tab.
  4. Uncheck Hide extensions for known file types if it is checked.
  5. Click on the Apply to All Folders button
  6. Click Yes
  7. Press OK in the Folder Options window.
File extensions are now enabled.

3. When working in Windows, make sure that your mouse pointer shadow is not enabled.

Mouse shadows can cause problems with OpenGL applications, and therefore, should be disabled when running PyMood (specifically the PyMood 3D Viewer)

To disable the mouse shadow in Windows 2000, follow these instructions:
Click on 'Start', point to 'Settings' and select 'Control Panel'
Double-click on 'Mouse' and click on the 'Pointers' tab
Uncheck 'Enable pointer shadow'

To disable the mouse shadow in Windows XP, use these instructions:
Click on 'Start', and then click on 'Control Panel'
Locate and click on 'Switch to Classic View' at the top-left (if in the XP-style view)
Double click on 'Mouse'
Click on the 'Pointers' tab
Uncheck 'Enable pointer shadow'

4. Windows in PyMood may take a few second to close. Please be patient as the programs free their memory resources.

5. While working in PyMood on Windows do not close the terminal window. By closing this window, you will exit PyMood. This window may be minimized.