MOL2 Support in PyMOL
The MOL2 file format specification can be downloaded from Tripos can be as a PDF file.
PyMOL implements a small subset of this format in order to permit loading of molecular structures from Sybyl into PyMOL.
The primary advantage of using MOL2 is that it is one of the few public formats capable of supporting both a chemically-accurate description of a molecular system that contains both small organic molecules and a large number of protein or nucleic acid atoms. However, the requirement for atom type specifications has so far prevented addition of MOL2 output support into PyMOL.
As of January 2007, MOL2 support in PyMOL is still relatively young and unproven – it needs more “beating on”. So, if you encounter problems reading your MOL2 files into PyMOL, please contact Support so that we can troubleshoot and hopefully solve the problem.
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