[Chimera-users] showing density from Gaussian in Chimera

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 3 16:48:25 PDT 2016


Hi Ana Maria,
After you click or move the slider in the histogram in Volume Viewer, the number is shown in that same dialog next to “Level”, or you can just type in the number you want there.  For an example, see the figure in the link I sent before:

> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#dispsurf>

In the figure, it shows that the isosurface level is 119.
Best,
Elaine

On Jun 3, 2016, at 1:15 PM, Mendoza Wilson, Ana Maria <mwilson at ciad.mx> wrote:

> 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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