RE: plotting 3D electron density difference maps
- From: "DeLano, Warren" <warren-: at
- Subject: RE: plotting 3D electron density difference maps
- Date: Mon, 18 Mar 2002 13:59:59 -0800
> From: Anik Peeters [mailto:anik-: at :-uia.ua.ac.be]
> I am looking for software, preferably freeware, to plot 3D electron
> density or electron density difference maps for large molecules (appr.
> 500 atoms). The program may run on a unix workstation or on pc.
PyMOL is ideal for this kind of project, where you might be able to do a
bit of development in order to enable efficient transfer of your 3D
dataset into the visualization program.
> We have our own programs to calculate the value of the
> electron density
> (difference) in the grid points of a given 3D lattice.
> Therefore, we can
> generate the results in any format needed, but we do need to know what
> the input format is for a given plotting program, so
> therefore we would
> prefer a program that comes along with its source code or sample input
> files. We also welcome programs for converting one 3D data set into
PyMOL can read XPLOR and CCP4 format electron density files, but you can
also create a 3D volume "brick" from within Python (using the
high-perfomance "Numeric" package) to display volume data like
density. Mesh isosurfaces are supported by the current binary release,
and the impending release supports solid isosurfaces too (source code in
current CVS). These are great for MO diagrams and/or electrostatic
Python is rapidly becoming a standard programming language for
computational chemistry, so I encourage everyone to learn it. PyMOL's
capabilities provide you with a specific reward for doing so.
> I already donwloaded Molden, but it seems a bit slow when I am looking
> at our molecular system interactively.
Provided that you can access a graphics accelerator card, PyMOL's
performance meets or beats any other package, and it is cross-platform
(Windows, Unix, MacOSX). It can display any 3D map that will fit into
And now for the best part...
PyMOL is unrestricted open-source software (even for commercial usage),
meaning that it is free, modifiable, and redistributable in modified
form. If you find PyMOL useful, then you are asked to help advance the
project through development, documentation, or funding. PyMOL's users
(hundreds of scientists distributed around the globe) are working
together to make it a better and better package each and every day.
Everyone is welcome to join the effort.
The goal of PyMOL is to create the "Linux" of molecular modeling: a
Python environment, (including PyMOL and other powerful packages), that
is free, open-source, interoperable, and suited for an unlimited variety
of tasks in computational chemistry and structural biology.
mailto:warren-: at :-sunesis.com
Warren L. DeLano, Ph.D.