[chimerax-users] Reading cube file from Quantum Espresso pp.x

[Elaine Meng]

Hi Zack,
A cube file is a map format (values at points on a regular grid), and is not used for atomic coordinates.  In other words, I believe your file contains only the wavefunctions. You would need to also open a file for the atomic coordinates (possible formats PDB, SDF, MOL, ...) which you may have input to Quantum Espresso, or may be able to write from the program.  I've never used it, so I don't know what it writes.

ChimeraX knows these atomic formats:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic>
... and these map formats:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume>

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

> On Feb 2, 2021, at 9:45 AM, Zack Gainsforth <zackg at berkeley.edu> wrote:
> 
> Hi,
> 
> I produced some projected wavefunctions in a crystal that I'm working with using Quantum Espresso (DFT).  I output these projections to a gaussian cube file using the pp.x program (built into Quantum Espresso).  I'm able to read these into ChimeraX but I'm unable to see the atoms -- only the volumetric data.  I tried Actions - Atoms/Bonds - Show, but I still don't see the atoms. Is there another step I should take to make them visible?
> 
> I see something like this:
> 
> <PastedGraphic-1.png>
> 
> (very nice!)
> 
> I'm attaching a link to the cube file below -- I can't include it because it is 600 MB.
> 
> Thanks,
> 
> Zack
> 
> https://www.dropbox.com/s/ehhli8h3qr7vd4y/wfc_k001_b329wfc.cube?dl=0