Re: [PyMOL] Pymol capabilities

[DeLano S. <de...@de...>]

Jack,
 
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.
 
Cheers,
Warren
 
--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...

  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of Jack Shultz
Sent: Wednesday, February 13, 2008 11:43 AM
To: pym...@li...
Subject: [PyMOL] Pymol capabilities


Hello,

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. 

Jack