Advanced Scripting Workshop

Part 2: How to run scripts conveniently...

With PyMOL 2.0 on all platforms

Drag the .pml script from Explorer/Finder/Dolphin etc. into PyMOL window.

... on Linux

Using a terminal (e.g. xterm):

1. cd to the directory where you have your script and/or data
2. Run PyMOL with the script:

   # run a PyMOL command script (opens PyMOL GUI)
   pymol script.pml
   
   # run a Python script
   pymol script.py
   
   # batch mode (no PyMOL GUI)
   pymol -c script.pml
   
   # use absolute path if "pymol" is not in $PATH
   /opt/pymol-2.2.3/pymol -c script.pml

... on Mac

• Using Finder: Drag the .pml script over the PyMOL icon in the dock.
• Using a terminal (e.g. Terminal.app): Same as on Linux.
  Put an alias like this in your ~/.bashrc:

  alias pymol=/Applications/PyMOL.app/Contents/MacOS/PyMOL

... on Windows

Register .pml extension with PyMOLWin.exe

• PyMOL 2.x: Setting > Register Extensions
• PyMOL 1.x: During Installation (default)

Using Windows Explorer:

1. Create a PyMOL application shortcut on the Desktop.
2. Drag the .pml script to the application shortcut.

... from the PyMOL command line

Load PML scripts with @:

PyMOL> @example.pml

PyMOL> @/tmp/PyMOLScripts/example.pml

PyMOL> @C:\PyMOLScripts\example.pml

Load Python scripts with run:

PyMOL> run example.py

PyMOL> run /tmp/PyMOLScripts/example.py

PyMOL> run C:\PyMOLScripts\example.py

Open a Script with PyMOL

Download the PyMOL (PML) script example.pml and open it with PyMOL by dragging it into the PyMOL window.

Expected result:

Run a script with the PyMOL command line

Run the same example.pml script on the PyMOL command line with @.

Hints: The commands cd, pwd and ls are useful to first navigate to the right directory. Filename auto-completion speeds up typing and avoids typos. You can also use environemnt variables (e.g. $HOME) and ~ (home directory).

Run a Python script from the PyMOLWiki

1. Download and run bbPlane.py from https://pymolwiki.org/index.php/BbPlane. For example like this:

   run ~/Downloads/bbPlane.py

2. Load a protein structure, e.g. by typing into the PyMOL command line:

   fetch 1ubq

3. The bbPlane.py script added the new bbPlane command to PyMOL, type it into the PyMOL command line and hit Enter

   bbPlane

Expected result:

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