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This is a guide intended to help you install and manage the Bio-Prodict 3DM PyMol Plugin in PyMol 2.
PyMol includes an easy-to-use plugin repository that lets you effortlessly download and install the Bio-Prodict 3DM PyMol Plugin. The latest stable version number can be found here.

This is the documentation for installation under PyMol 2.3x. You may find the installation instructions for 1.8.x here.

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You need PyMol to run this plugin. We support the 1.8.x and the 2.3.x version of PyMol at this time.
Download the PyMol binaries from PyMol.org, or get the source from SourceForge.net and build the program yourself.

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  1. Start PyMol
  2. Click on Pluginin the control window (the top menu bar in MacOS)
  3. Select Plugin Manager from the dropdown
  4. In the Plugin Manager window, go to the Install new plugin tab.
  5. Click on Add in the lower left of the window.
  6. Enter the URL for the repository you want use in the URL field and click okay.
    The 3DM plugin is released in these two versions. If you want to use the newest features, it is recommended that you pick the Edge repository. If you would rather have the best tested version, you can pick the Stable repository.
    Repository URLs:
  7. Select the repository from the Repositories list.
  8. Select the 3dm_plugin_<repository>.zip file in the Items list
  9. Confirm that you want to install into the default directory.
  10. Click Install
  11. Restart PyMol
  12. Open the 3DM plugin from the Plugin > Legacy Plugins menu.
  13. To test the PyMol-3DM connection, follow the instructions here.

If you encounter any problems during this installation, please proceed to the manual installation steps or look at common issues in the Troubleshooting chapter below.

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Once you have restarted PyMol, the 3DM plugin can be called from the Plugins menu. To test the PyMol-3DM connection, follow the instructions here.

Finding out my current plugin version

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  1. With Homebrew installed, launch a Terminal window.
  2. In this window, type the following instructions in order:
    • brew update
    • brew install openssl
    • brew link --force openssl
  3. If you had PyMol open, restart it.

Unable to retrieve version error

It may be that your company uses a self signed certificate to encrypt traffic inside the network. You must disable SSL verification for YASARA 3DM to work. For security reasons we do not recommend this recourse for computers that may move outside the company network.


1. Navigate to the location where you installed PyMol in Explorer. This is likely C:\Program Files\YASARA .
2. Inside this directory, navigate to plg\bioprodict
3. Open the config.json file in notepad (or your favorite plain text editor)
4. Find the line that says: "verify_https": true , change true to false to disable this setting.
5. Save the file.
6. Restart YASARA, the plugin should now work.


I am using MacOS and I can't copy/paste my credentials.

XQuartz binds copy/paste specifically to Ctrl+C/Ctrl+V as opposed to Cmd+C/Cmd+V.


I encounter an XQuartz error

XQuartz is a compatibility layer for OSX/MacOS that is required to launch the 3DM plugin. Please install XQuarts using the instructions on their website: https://www.xquartz.org/

I installed XQuartz and restarted my Mac, but I still get XQuartz errors

Make sure that your X11 libraries are installed correctly. You may need to symlink the install directory to the directory expected by PyMOL. This can be done by

  1. Opening a Terminal
  2. Typing: sudo ln -s /usr/X11 /usr/local/opt/libx11
  3. Pressing Enter
  4. Entering your password
  5. Restarting PyMol