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@cgl.ucsf.edu> on behalf of Eric Pettersen <pett@cgl.ucsf.edu> Sent: Wednesday, April 7, 2021 12:21 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Cc: Carles Serrat Jurado <carles.serrat-jurado@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@cgl.ucsf.edu> wrote:
Hi Carles, We recommend using the chimerax-users@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@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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