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PyMOL allows the execution of python commands from the PyMOL command line. It is very useful for both debugging, and for discovering new functions.

  • Any expression that is not recognized as a PyMOL command is passed to the underlying python interpreter
  • To force a one-line expression to be executed as python, begin the line with a slash (/)
  • Use the python command to input multi-line python code


# there is no "print" command in PyMOL, so this will go to the python interpreter
print "Hello World (1)"

# same, but force it to be python
/print "Hello World (2)"

# no lets trick this system by introducing a PyMOL command named "print"
cmd.extend('print', lambda msg: sys.stdout.write("You gave me `%s`\n" % (msg)))

# see what happens
print "Hello World (3)"

# this will still go to the python interpreter
/print "Hello World (4)"