[chimerax-users] ChimeraX reading cube files

[Elaine Meng]

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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