Common issues

As PyMOL is a quite complex software with a lot of its functionality written in C++, sometimes unexpected results or crashes may occur under certain circumstances. This page should provide help in such and similar cases.

Interactive PyMOL crashes when launched after usage of Matplotlib

Interactive PyMOL will crash, if it is launched after a Matplotlib figure is created. This does not happen in the object-oriented library mode of PyMOL. Presumably the reason is a conflict in the OpenGL contexts.

Example code that leads to crash:

import matplotlib.pyplot as plt
import ammolite

figure = plt.figure()

‘cmd.png()’ command crashes in pytest function

PyTest executes the test functions via exec(), which might lead to the crash. Up to now the only way to prevent this, is not to test the png() command in pytest.

Launching PyMOL for the first time raises DuplicatePyMOLException

For example the code snippet

from ammolite import cmd, launch_pymol



ammolite.DuplicatePyMOLException: A PyMOL instance is already running

The reason:

If from ammolite import pymol or from ammolite import cmd is called, PyMOL is already launched upon import in order to make the pymol or cmd attribute available. Subsequent calls of launch_pymol() or launch_interactive_pymol() would start a second PyMOL session, which is forbidden.

To circumvent this problem do not import pymol or cmd from ammolite, but access these attributes via ammolite.pymol or ammolite.cmd at the required places in your code.