[chimerax-users] ChimeraX reading cube files

[Carles Serrat Jurado]

Thanks a lot, Elaine, Eric and Anthony!

Carles
 

> On Apr 7, 2021, at 6:21 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> 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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> 

—————————-—————————
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
——————————————————-