VMD-L Mailing List

From: hinsen_at_dsm-mail.saclay.cea.fr
Date: Sun Dec 19 2004 - 03:04:09 CST

On 18.12.2004, at 22:29, Amarda Shehu wrote:

> does anyone have any experience with visualization and/or comparison of
> electron density map files?

Yes, I have done a lot of it recently.

I'd that VMD is not the best choice for density maps, at least not in
its current state. I have used both PyMOL and MayaVi, each has its
particular strong and weak points. MayaVi is not a molecular viewer at
all, it cannot display molecular structures, but it has many useful
functions to deal with 3D volume data, which is what an electronic
density is.

A big problem with electronic density data is the chaos about file
formats. There are lots of them and hardly any is properly documented.
The most popular format seems to be the CCP4 format, but I haven't seen
a description of it that does not take the form of a Fortran program. I
ended up decoding the file formats myself and write conversion code in
Python. I also do all the calculations on density maps in Python. Both
PyMOL and MayaVi let me feed volume data into them from Python code.

Konrad. 

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Konrad Hinsen
Laboratoire Leon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: hinsen_at_llb.saclay.cea.fr
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