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Installing Molekel and Configuring a file association for your Web Browser

To view the molecules on the free molecule viewer, MOLEKEL, please install the software from the following website. Note that the software is not available for Macintosh computers. By configuring your web browser as below, the web browser will recognize the files and open Molekel for you.

  1. Install Molekel (version 4.2 or later) --
    1. Move to: 'C:\Program Files\Molekel\' (assumes a modern Windows system)
    2. Rename executable to 'molekel.exe'.
    3. Make sure to add the directory to the PATH Environment variable.
      On Windows systems, click on the 'Help' item in the 'Start' menu and look for 'path' items in the Index list. There should be an entry for modifying the PATH Environment variable. Add the following path to the PATH variable (Note the use of the semi-colon as a separator):
         C:\Program Files\Molekel
      On Unix systems, ask your system administrator how to set your PATH variable.
    4. Check the value for Boron (B) in the '' file; change the value to '0.840000' if the value is '0.800000'.
    5. Copy library files to the 'C:\usr\local\lib\Molekel\' directory (Create required directories/folders if necessary.)
  2. If you do not currently have it, install glut.dll (or glut32.dll for windows) in the same folder as Molekel (See
  3. Test Molekel to ensure that it opens with two windows.
  4. To define an .mkl File Type (assumes .mkl extension is undefined.)
    - In Windows systems:
    1. For specific instructions for associating an 'mkl' file extension with its Molekel application on a Windows system, click on the 'Help' item in the 'Start' menu and look for 'extensions' in the Help index. There should be a 'To create or modify a file type' entry with instructions.
    2. As a file description, use 'MKL file'
    3. If you are asked to fill in a MIME type field, use 'chemical/x-molekel-input'
    4. Be sure to type the following in the application field:
      "C:\Program Files\Molekel\molekel.exe" -mkl "%1"
      (Include the quotation marks above.)

    - In old versions of the Netscape browser:
    1. On the Edit menu, click Preferences
    2. On the Navigator menu, choose Applications
    3. Choose New
    4. Enter the following
      1. Description: MKL file
      2. MIME Type: chemical/x-molekel-input
      3. Extension (or Suffix): mkl
    5. In the application field, type:
      "C:\Program Files\Molekel\molekel.exe" -mkl "%1"
      (Be sure to include the quotation marks above. In some browsers, it may be necessary to type Ctrl+Alt+space to get a space in the field.)
    6. Click OK