[Chimera-users] viewing Gaussian files

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 21 09:20:33 PST 2012

Hi Valia,
Chimera can read atomic structures from .fchk files, and "volume" data (values on grid points such as electron densities) from .cube files.  You can just use File... Open in the Chimera menu if the files are named with those suffixes.  Chimera input file types:

However, I am not sure if the information written by Gaussian to the cube file is electron (probability) density or electrostatic potential, or whether you have the choice.  Make sure you know what the volume data in the cube file really is.  If it is indeed electrostatic potential, in Chimera, you can display isopotential contour surfaces with the Volume Viewer tool, or show the values of the potential with color on the molecular surface of the atomic structure using the Surface Color tool (aka Electrostatic Surface Coloring).

Volume Viewer:

Surface Color:

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 21, 2012, at 6:44 AM, Valia Dimitrova wrote:

> Hi,
> I am PhD student, and I am working with program Gaussian, I want ask you some questions.
> I want to make maps with electrostatic potential, I saw that with this program may be make very beautiful pictures.
> What type of files I have to have, so I can do these pictures? I have ".fchk" files and ".cube" files. May I use them to make this? 
> I will be very appreciated if some one can help me.
> thank you in advance
> Valia Nikolova

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