[Chimera-users] showing density from Gaussian in Chimera

Mendoza Wilson, Ana Maria mwilson at ciad.mx
Fri Jun 3 13:15:19 PDT 2016

Elaine Meng,

Thank you very much for your advice. Where I could see if the isodensity
values is 0.004 or 0.0004?

Best regards

Ana María

2016-06-02 13:52 GMT-07:00 Elaine Meng <meng at cgl.ucsf.edu>:

> 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
> >

Dra. Ana María Mendoza Wilson
Investigador Titular
Centro de Investigación en Alimentación y Desarrollo, A.C.
Coordinación de Tecnología de Alimentos de Origen Vegetal
Carretera a La Victoria Km. 0.6
Hermosillo, Sonora, México
C.P. 83000
Tel +52 (662) 289 24 00 Ext. 354
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