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.
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.