[chimerax-users] ChimeraX reading cube files

[Elaine Meng]

Hi Carles,
We recommend using the chimerax-users at cgl.ucsf.edu address (CC'd here) for questions about ChimeraX, unless you have attached data that needs to stay private.

ChimeraX reads cube format but only as maps (e.g. density maps, electron localization functions, ...) with values on a grid.  It does not read atomic coordinates from the cube format.

This is a list of the atomic formats ChimeraX can read -- can you output any of those atomic formats instead of cube? (pdb, mol2, mol, sdf)
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic>

You can see that "cube" is in the list for volume (map) formats, but not as an atomic format.
<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 Apr 7, 2021, at 7:25 AM, Carles Serrat Jurado <carles.serrat-jurado at upc.edu> wrote:
> 
> Dear Elaine,
> 
> I am writing because I have problems to plot a cube file with ChimeraX. I would greatly appreciate your assistance. Here I send the only figure I get when I open the cube file with ChimeraX. Also I attach what I would more expect, which is obtained with the software VESTA.  
> 
> My ultimate goal is to make a movie with using different frames. I also send a zipped file with the frames, so that you can see the kind of cube files I am working on.
> 
> Thank you very much in advance for your support.
> 
> Best regards,
> 
> Carles
> 
> <ChimeraX.png>
> 
> <VESTA.png>
> <cube_files.zip>
> —————————-—————————
> Prof. Carles Serrat (PhD)
> Department of Physics
> UPC - Polytechnic University of Catalonia
> Colom 11, 08222 - Terrassa
> Phone: +34 93 739 8137  
> Mobile: +34 696 738 728
> https://donll.upc.edu
> ——————————————————-