Run Python Statements from PyMol

Molecule Tutorials - Herong's Tutorial Examples

∟Run Python Statements from PyMol

This section provides a tutorial on how to Run Python Statements from PyMol.

PyMol allows you to run Python statements automatically, if you have Python installed on your system.

If you just want to run a single Python statement, just enter the statement as is at the "PyMOL>" prompt or in a command script: For example:

PyMOL> print 1 + 2
3

If you want to run a statement block, then you need to add a backslash ('\') at the end of each statement except the last statement. For example:

PyMOL>for a in range(1,6): \
PyMOL>   b = 6 - a \
PyMOL>   print(a, b)
1 5
2 4
3 3
4 2
5 1

Note that you can not use PyMol commands inside a Python statement block. For example, if you try to turn the camera in a loop, you will get an error.

PyMOL>for a in range(1, 36): \
PyMOL>   turn y, 10
  File "toplevel", line 2
    turn y, 10
         ^
SyntaxError: invalid syntax

Python variables are not allowed in PyMol commands either:

PyMOL>angle = 45
PyMOL>turn y, angle
Traceback (most recent call last):
  File "/Applications/PyMOL.app/.../viewing.py", line 1411, in turn
    r = _cmd.turn(_self._COb,str(axis),float(angle))
ValueError: could not convert string to float: 'angle'