[Chimera-users] showing density from Gaussian in Chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 2 13:52:09 PDT 2016


Hello,
You can just open the file in Chimera, if it is in the proper format.  

I see that fchk and Gaussian cube grid are both possible input types:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>

However, only the atomic coordinates are read from an fchk file, whereas the cube format is used for volume data (values on a grid) like densities or orbitals.  Since you said “isodensity value” I am guessing you would need to have the cube format. You can just open that file (name ending in .cube or .cub) with menu: File… Open, and the data will automatically be shown as an isosurface in the main window, and the Volume Viewer tool will appear.  To change the isodensity level you can just drag the vertical bar slider on the histogram in the Volume Viewer tool, or type in a new number in the “Level” field. 

You can click the Help button to see more detailed information on this tool, or view it on our website here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#dispsurf>

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

> On Jun 2, 2016, at 10:03 AM, Mendoza Wilson, Ana Maria <mwilson at ciad.mx> wrote:
> 
> Hello,
> How I can select an isodensity  value in the Chimera software (1.11rc)  for calculating molecular surface and molecular volume from one cube data file or fchk file previously generated in Gaussian 09?  
> Thanks in advance
> 




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