Versions Compared

Old Version 9

changes.mady.by.user Stephan Heijl

Saved on

compared with

New Version 10

changes.mady.by.user Stephan Heijl

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

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.

...

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 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