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<span style="font-family: Arial, Helvetica, sans-serif;">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:
</span><a href="https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html" id="LPlnk481052"><span style="font-family: Arial, Helvetica, sans-serif;">https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html</span></a><br>
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<span style="font-family: Arial, Helvetica, sans-serif;">Tony</span><br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> Wednesday, April 7, 2021 12:21 PM<br>
<b>To:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Cc:</b> Carles Serrat Jurado <carles.serrat-jurado@upc.edu><br>
<b>Subject:</b> Re: [chimerax-users] ChimeraX reading cube files</font>
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<div class="PlainText">[EXTERNAL SENDER - PROCEED CAUTIOUSLY]<br>
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Hi Carles,<br>
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.<br>
<br>
--Eric<br>
<br>
Eric Pettersen<br>
UCSF Computer Graphics Lab<br>
<br>
<br>
> On Apr 7, 2021, at 8:54 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:<br>
><br>
> Hi Carles,<br>
> 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.<br>
><br>
> 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.<br>
><br>
> 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)<br>
> <<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats">https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats</a>><br>
> <<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic">https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic</a>><br>
><br>
> You can see that "cube" is in the list for volume (map) formats, but not as an atomic format.<br>
> <<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume">https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume</a>><br>
><br>
> I hope this helps,<br>
> Elaine<br>
> -----<br>
> Elaine C. Meng, Ph.D.<br>
> UCSF Chimera(X) team<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
><br>
>> On Apr 7, 2021, at 7:25 AM, Carles Serrat Jurado <carles.serrat-jurado@upc.edu> wrote:<br>
>><br>
>> Dear Elaine,<br>
>><br>
>> 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.<br>
>><br>
>> 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.<br>
>><br>
>> Thank you very much in advance for your support.<br>
>><br>
>> Best regards,<br>
>><br>
>> Carles<br>
>><br>
>> <ChimeraX.png><br>
>><br>
>> <VESTA.png><br>
>> <cube_files.zip><br>
>> ¡X¡X¡X¡X¡X¡X¡X¡X¡X-¡X¡X¡X¡X¡X¡X¡X¡X¡X<br>
>> Prof. Carles Serrat (PhD)<br>
>> Department of Physics<br>
>> UPC - Polytechnic University of Catalonia<br>
>> Colom 11, 08222 - Terrassa<br>
>> Phone: +34 93 739 8137<br>
>> Mobile: +34 696 738 728<br>
>> <a href="https://donll.upc.edu">https://donll.upc.edu</a><br>
>> ¡X¡X¡X¡X¡X¡X¡X¡X¡X¡X¡X¡X¡X¡X¡X¡X¡X¡X-<br>
><br>
><br>
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