Hello!
I have generated a .cube file using Quantum Espresso. How can I vizualize it please?
If you open the .cube file, the molecule will be read, and the cube/orbital can be displayed with the “Surfaces” rendering option.
I have a file named acetone.cube and I am trying to open it with this
extension but I cannot do it. even if I delete the .cube extension it does
not work.
Thank you
Gangotri Dey
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254
You’ll have to provide me with a bit more information.
- What version of Avogadro are you using?
- What OS are you using?
- Can you post the exact file (or a link to it)?
This works for me, which is why I’d like to see what’s going on. Thanks.
Here is the file.
Thank you
Gangotri Dey
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254
There is nothing here.
Did you try to e-mail the file to the discussion board? It won’t take attachments.
Try posting a URL for the file.
Please don’t post the text of the file. The formatting of the discussion board will corrupt it.
Please upload to Box or Dropbox or Google Drive or something and post the URL to the file or e-mail me directly.
Sorry!
It is in google drive now. Can you see it?
https://drive.google.com/file/d/0B4OAPX8yxfiZa2p4N2tOWHB4RWc/view?usp=sharing
Thank you
Gangotri Dey
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254
Dear colleagues,
I have a similar problem. Avogadro can load cube file but only the molecular structure (bonds and atoms) are rendered. Orbital isosurface does not appear. Same file in VESTA is plotted with orbital. I tried most recent version of Avogadro, both Mac and Win. The cube file can be downloaded from
https://gigamove.rz.rwth-aachen.de/d/id/Xy9bpuKQzptz7L
I would recommend trying Avogadro2 - while it’s still in development, it has no problems with your cube file:
The latest Mac build is here - we’ll shortly release a 1.94 binary: https://github.com/OpenChemistry/avogadrolibs/suites/637580336/artifacts/5283787
Thank you, but your link follows to “404”. Meanwhile I found another solution for my version of Avogadro via Extensions->Create Surfaces
Go to extensions > create surfaces > change isovalue to 0.001 > calculate. Works for me!