[chimerax-users] Difficulties Visualizing Isosurfaces from Cube File - Nathan Wood

[Elaine Meng]

Hi Nathan,
The previous posts aren't that relevant... April 2021 doesn't apply unless your cube file contains atomic coordinates that you are trying to view.  The relevant part of the May 2020 post is:
"If you open a .cube file it will automatically show as isosurfaces."

You could still use the Volume Viewer interface after that to adjust the isosurface levels and their colors, of course.

Don't know what you mean by "from the shell" or "difficulties" or "incompletely visualize" though.  You can first start ChimeraX and then use its File... Open menu, or the "open" command, e.g. "open browse" if you want to use a file browser interface to locate your cube file.  Make sure you are using a reasonably new ChimeraX, e.g. the latest production release.

If that doesn't show isosurfaces, I couldn't say anything else unless you provide the cube file itself and probably also give more details about what exactly is problematic.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 12, 2021, at 7:43 PM, Nathan Wood via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX
> 
> I was having difficulty attempting to visualize computationally
> generated electrostatic potential isosurfaces originating from a
> Gaussian *.cube file.
> 
> I tried to open the cube file from the shell only for it to incompletely
> visualize. I can provide an image if necessary.
> 
> I found the following correspondence concerning cube files and
> isosurfaces, but unfortunately I am unable to resolve the issues of the
> cube file visualizing.
> 
> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-April/002126.html
> <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-April/002126.html>
> 
> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001110.html
> <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001110.html>
> 
> 
> I was curious if anyone has had experience with cubefiles.
> 
> Any assistance would be greatly appreciated,
> 
> Very Respectfully,
> 
> Nathan Wood
> 
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