Although not everyone sees PyMOL in such a narrow light, my view is that the software is best viewed as a molecular graphics platform open for integration with computational tools (e.g. semi-empirical QM/MM) via manual data import, via automated PyMOL command scripts, or via the Python programming language. 
Although limited geometric analysis are possible via PyMOL's commands and API, PyMOL is not a standalone tool for doing computational chemistry, or structural biology, or bioinformatics.
But if you have QM/MM tools which output molecular structures and volumetric maps, then it should be possible to load such content into PyMOL for visualization and animation, and for sharing results with your scientific colleagues.
DeLano Scientific LLC
Subscriber Support Services

From: pymol-users-bounces@lists.sourceforge.net [mailto:pymol-users-bounces@lists.sourceforge.net] On Behalf Of Jack Shultz
Sent: Wednesday, February 13, 2008 11:43 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Pymol capabilities


I am learning a little about molecular dynamics simulations. Currently using Amber and CP2k. Hoping to integrate CP2K into a distributed computing project using serialized computations. A friend of mine recently said Pymol is a fancy piece of software. Before I get invested in learning about it, I want to know its relevance to what I hope to do. I want to model chemical reactions and study their intermediate stages. I am looking for computationally light tools. Ones that use Semi-Empirical QM/MM.