[chimerax-users] ChimeraX reading cube files
Carles Serrat Jurado
carles.serrat-jurado at upc.edu
Sat Apr 10 11:05:12 PDT 2021
Dear Elaine,
I got it! This is working, thanks so much!
Carles
> On Apr 10, 2021, at 6:01 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
>> On Apr 10, 2021, at 7:54 AM, Carles Serrat Jurado <carles.serrat-jurado at upc.edu> wrote:
>>
>> Dear Elaine,
>> Thank you very much for your help. These instructions will certainly be very important for my work.
>>
>> There is still something that is not clear to me. My cube files, produced by the NWChem package, include information about the differential density. This appears by default when I open one of these files with the VESTA visualization software (https://jp-minerals.org/vesta/en/). Here I attach the 10 cube files I sent to you just converted to tif images after opening them with VESTA. As you can see, it is not the position of the atoms what evolves, as you already observed, but the differential charge density.
>>
>> I don’t know why ChimeraX does not produce the differential densities. If it would do it, then following your kind indications I could make now a movie to see that evolution (I have thousands of cube files to see a quite long time evolution - 5 femtoseconds, actually :-), which is what I am looking for.
>>
>> Again, I sincerely thank you for your answers and indications. I understand that probably ChimeraX is not able to read this information from my cube files.
>>
>> Best regards,
>> Carles
>>
>> PS: Please no worries about the data I am sending, it is not private so to say, these are tests I am doing at the moment.
>> PS2: I subscribed to the ChimeraX mailing list, but I don’t manage yet to answer there and attach files, please be free to share my mails however.
> <tif_files.zip>
>
> Dear Carles,
> From your first message, I mistakenly thought you only wanted to see the atomic coordinates, so I ignored the density part. The instructions I sent before were how to make an atomic trajectory. If the atoms don't change position, then you can ignore most of those long instructions and just make one atomic model and keep showing it at the same time you show the changing density. For example, just open the attached PDB file, carles1.pdb.
>
> By default, ChimeraX does show the density from the cube files... that is the blob you see as soon as you open the file. If you mean that you want to see the densities as a series that changes over time, you just need to use the "open" command "vseries" option to tell ChimeraX that it is a volume series.
>
> For example, you previously sent a folder containing 10 files named density_subgs.0000030000.cube .... density_subgs.0000039000.cube (numbering increments of 1000). In ChimeraX, the following command opens the 10 files as a single volume series (time series):
>
> open [folder location]/density*cube vseries true
>
> Now you have a slider to play the series, or you can use the "vseries" command. Screen shot below.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html>
>
> More about atomic trajectories and volume series:
> <https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html>
>
> The blob is probably bigger than what you are used to seeing in Vesta. This is just the contour level. To change contour level, you can move the vertical bar on the volume viewer (density map) histogram that automatically appears when you open the data in ChimeraX.
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html>
>
> Your cube files are signed data, so there are two vertical bars, one for the positive contour level and one for the negative contour level. You can drag either bar, and change the color by then clicking on the small color square above the histogram. In the attached screenshot I made the negative one greenish and the positive one magenta. I only see a very small change in these densities as I play the 10 frames.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> <carles1.pdb><Screen Shot 2021-04-10 at 8.57.22 AM.png>
>>
>>
>>
>>> On Apr 10, 2021, at 3:10 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>>
>>> Hi Carles,
>>> Attached is the PDB file from step #3 that you can open as a trajectory as described in step #4.
>>> Best,
>>> Elaine
>>>
>>> <carles-atomic.pdb>
>>>
>>>
>>>
>>>> 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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>>>>>>
>>>>>
>>>>>
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>>>>
>>>>
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>>
>> —————————-—————————
>> 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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—————————-—————————
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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