[chimerax-users] ChimeraX reading cube files

[Anthony James Schaefer]

ChimeraX does actually store the atom info in the cube file. Someone asked about this a while ago, and it was mentioned that there's some limitation where the stuff for opening volume data can't load atomic structures or something. I can't find the thread, but Tom Goddard wrote a script to load those atoms into ChimeraX: https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html

Tony
________________________________
From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of Eric Pettersen <pett at cgl.ucsf.edu>
Sent: Wednesday, April 7, 2021 12:21 PM
To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Cc: Carles Serrat Jurado <carles.serrat-jurado at upc.edu>
Subject: Re: [chimerax-users] ChimeraX reading cube files

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


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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