[chimerax-users] ChimeraX reading cube files

[Eric Pettersen]

Hi Carles,
	I'm no Gaussian expert, but the SEQCROW tool can read Gaussian log files, which might help.  You can download SEQCROW from the ChimeraX Toolshed, which you can access via Tools→More Tools... in ChimeraX.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Apr 7, 2021, at 8:54 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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
>> ——————————————————-
> 
> 
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