[chimerax-users] Reading cube file from Quantum Espresso pp.x

Tom Goddard goddard at sonic.net
Tue Feb 2 11:51:44 PST 2021 

Hi Zack,

  There is a line of code in the Python script that makes the wrong bonds

	s.connect_structure()

that you can comment out by putting a "#" character in front of it.

	# s.connect_structure()

Then it will just create the atoms and not the bonds.  Thanks for mentioning the wrong indentation -- there were tabs in the code in the web page that got translated into 4 spaces instead of 8 -- I have fixed it by using all spaces.

  I made a feature request to improve the Gaussian cube reader to also make the atoms.  It is a bit tricky to squeeze in because the current code is a volume data reader that can only return volume data.  Busy working on a grant now, so will have to wait.

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

  Tom

> On Feb 2, 2021, at 11:39 AM, Zack Gainsforth <zackg at berkeley.edu> wrote:
> 
> Hi Tom,
> 
> Sorry if I got my cube files crossed up!  I’m comparing several at the present so I must have just mixed it up.
> 
> The latest image you sent looks correct, except for the bonds as you note.  (It’s a spinel.)  However, the projected orbitals look correct, so the code is superimposing the volumetric data on the atomic data correctly.  I tried it your script and it works terrifically!  (Although I think some indentation got lost in the post on github.)
> 
> I simply turned off the metallic bonds and wound up with (yet another cube file):
> 
> <PastedGraphic-2.png>
> 
> Thank you much!
> 
> Cheers,
> 
> Zack
> 
>> On Feb 2, 2021, at 11:19 AM, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>> 
>> Hi Zack,
>> 
>>   Elaine is right that ChimeraX only reads the map in Gaussian cube files, not the atoms.  I was curious what your atoms looked like so I wrote a short Python script to make the atoms from your file and put it on the ChimeraX Recipes web site as an example of ChimeraX Python code.
>> 
>> 	https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html <https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html>
>> 
>>   The Gaussian cube file you linked to in your original message is not the same as the one you show in your second message.  In the linked file I see a lattice of aluminum, magnesium and oxygen.  ChimeraX tries to make metal coordination bonds (purple dashed lines) and put bonds between various aluminum atoms and made a pretty bizarre and likely wrong picture.  ChimeraX is designed for proteins so doesn't know what to do with inorganic crystals.
>> 
>> 	Tom
>> 
>> <wfc_K001_B329wfc.png>
>> 
>>> On Feb 2, 2021, at 10:42 AM, Zack Gainsforth <zackg at berkeley.edu <mailto:zackg at berkeley.edu>> wrote:
>>> 
>>> Hi Elaine,
>>> 
>>> Thanks for the feedback!
>>> 
>>> I think it does contain atomic coordinates because if I open the file up, the first few lines say:
>>> 
>>>  Cubefile created from PWScf calculation
>>>  k_point    1, band  493
>>>   112    0.000000    0.000000    0.000000
>>>   360    0.000000    0.043010    0.043010
>>>   360    0.043010    0.000000    0.043010
>>>   360    0.043010    0.043010    0.000000
>>>    13   13.000000   15.550626    7.919837   23.249520
>>>    13   13.000000    7.794637   15.500714   23.173025
>>>    13   13.000000   15.344622    7.808598    7.696103
>>>    24   24.000000    8.153563   23.302893   15.676357
>>>    24   24.000000   22.842015   15.147909   23.267895
>>>    24   24.000000   23.276582   23.168925   15.892733
>>>    24   24.000000    0.413132   15.595221   15.687712
>>>    13   13.000000   15.337306   19.401078   19.211118
>>>    24   24.000000   23.238956   26.684104   19.354277
>>>    13   13.000000   30.836280   19.498740   19.483616
>>>    13   13.000000   23.156913   11.704068   19.344564
>>>    13   13.000000    7.845982    3.847472   11.610165
>>> 
>>> So we have 13 being magnesium, and 24 being Cr, etc.
>>> 
>>> After the 112 atoms, it starts with the volumetric values.
>>> 
>>> So it sounds like perhaps I should request a feature addition to ChimeraX to implement atomic coordinates as well? 
>>> 
>>> Following your advice though, I saved the structure as a pdb also, and loaded that and it seems to work — though there is an offset between the volumetric and atomic datasets.
>>> 
>>> <PastedGraphic-1.png>
>>> 
>>> I guess I would need to manually shift one of them, so that provides a workaround for now.
>>> 
>>> Thanks,
>>> 
>>> Zack
>>> 
>>>> On Feb 2, 2021, at 10:15 AM, Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>> wrote:
>>>> 
>>>> Hi Zack,
>>>> A cube file is a map format (values at points on a regular grid), and is not used for atomic coordinates.  In other words, I believe your file contains only the wavefunctions. You would need to also open a file for the atomic coordinates (possible formats PDB, SDF, MOL, ...) which you may have input to Quantum Espresso, or may be able to write from the program.  I've never used it, so I don't know what it writes.
>>>> 
>>>> ChimeraX knows these atomic formats:
>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic>>
>>>> ... and these map formats:
>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume <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 Feb 2, 2021, at 9:45 AM, Zack Gainsforth <zackg at berkeley.edu <mailto:zackg at berkeley.edu>> wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> I produced some projected wavefunctions in a crystal that I'm working with using Quantum Espresso (DFT).  I output these projections to a gaussian cube file using the pp.x program (built into Quantum Espresso).  I'm able to read these into ChimeraX but I'm unable to see the atoms -- only the volumetric data.  I tried Actions - Atoms/Bonds - Show, but I still don't see the atoms. Is there another step I should take to make them visible?
>>>>> 
>>>>> I see something like this:
>>>>> 
>>>>> <PastedGraphic-1.png>
>>>>> 
>>>>> (very nice!)
>>>>> 
>>>>> I'm attaching a link to the cube file below -- I can't include it because it is 600 MB.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Zack
>>>>> 
>>>>> https://www.dropbox.com/s/ehhli8h3qr7vd4y/wfc_k001_b329wfc.cube?dl=0 <https://www.dropbox.com/s/ehhli8h3qr7vd4y/wfc_k001_b329wfc.cube?dl=0>
>>>> 
>>> 
>>> _______________________________________________
>>> ChimeraX-users mailing list
>>> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
>>> Manage subscription:
>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
>> 
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20210202/f2ac2100/attachment.html>

More information about the ChimeraX-users mailing list