[chimerax-users] ChimeraX reading cube files

[Tom Goddard]

There is a ChimeraX feature request for having the CUBE file reader show both the map and the atomic model.

	https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4207 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4207>

I am not sure when that will get done, so for now the ChimeraX recipes script can be used.

	Tom

> On Apr 9, 2021, at 6:07 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Dear Carles,
> It took me a couple of days to try that recipe script on your data, sorry about the slow reply.  Now I realize there are a few extra steps to convert your data to a trajectory (e.g. with slider to play as movie), so I thought I should share the details with the list:
> 
> (1) In ChimeraX, I opened your 10 cube files, and then I used the python file in the ChimeraX recipe to create 10 atomic models.
> <https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html>
> 
> (2) Then I saved the 10 atomic models as a single PDB file (using ChimeraX menu: File... Save), File type PDB, relative to the first atomic model.  Doesn't matter which one you choose as the "relative to" model, however.
> 
> (3) Then I was going to open that single PDB file as a trajectory.  However, there is a bug in the saving that currently prevents it.  The bug puts "END" after each atomic structure in the file.  So I first needed to text-edit the PDB file to remove all of the "END" lines (but not "ENDMDL").  
> 
> **I will send you the resulting PDB file in a separate message in case it is private data.**
> 
> (4) In ChimeraX, I closed all the other models and then opened the new edited multi-model PDB file with the "coordsets" option to make it into a trajectory, for example, command:
> 
> open carles-atomic.pdb coordsets true
> 
> However, 10 frames of the trajectory all look exactly the same to me, but far as I know that is a correct conversion of the data from the 10 cube files you sent me.
> 
> When the bug is fixed (#4487 <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4487>), step #3 would not be necessary.
> 
> 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 9:33 AM, Anthony James Schaefer <tony.schaefer at uga.edu> wrote:
>> 
>> 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
>> 
>>> 
>>>> 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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