Author Topic: Virus detection  (Read 206 times)

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Offline asma

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Virus detection
« on: March 10, 2020, 11:46 »
My plan is to build a field effect transistor using quantumwise software to detect viruses such as (HIV-influenza A). Does quantumwise database provide me with the required atoms or molecules to build the virus?


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Asma

Offline NW

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Re: Virus detection
« Reply #1 on: March 13, 2020, 17:24 »
Hi,

I converted the HIV virus *.cif file that I got from: https://www.rcsb.org/3d-view/4XFZ to *.py file.

You can download it here and then import it into VNL.

Since I am not expert at HIV virus, please check the link and structure before doing your simulations.

 

Offline asma

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Re: Virus detection
« Reply #2 on: March 16, 2020, 06:59 »
Many Thanks

Offline asma

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Re: Virus detection
« Reply #3 on: March 29, 2020, 09:57 »
I would like to ask how did you convert .cif file to python file.
I'm trying with other types of viruses but I'm not getting it right.

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Offline Petr Khomyakov

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Re: Virus detection
« Reply #4 on: March 30, 2020, 13:02 »
Having an example cif file posted would be helpful. In general, converting might be tricky, as not everybody sticking to conventions when creating those.

Offline asma

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Re: Virus detection
« Reply #5 on: April 1, 2020, 12:17 »
Thanks for your reply.
I want to get the python script for the rotavirus displayed in the following link:
http://www.rcsb.org/3d-view/4V7Q
 
I was able to download the cif file but I couldn't convert it to python.
Please advise how to convert it?

Offline Petr Khomyakov

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Re: Virus detection
« Reply #6 on: April 1, 2020, 21:52 »
The cif-file is 606Mb. Do you really want to model a structure with millions of atoms?

Offline asma

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Re: Virus detection
« Reply #7 on: April 2, 2020, 07:32 »
I didn't realize that it has millions of atoms.
The truth is that I'm still in the first step (proposal) in this research idea. I want to make sure that I'll be able to design the virus using quantumwise and that the simulation time for each run  will be reasonable. I'm using high performance computer.
Below is another link for a much smaller file:
http://www.rcsb.org/structure/3MIW

Can you provide me with link, tutorial, or explanation to convert cif file to python.

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Offline Petr Khomyakov

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Re: Virus detection
« Reply #8 on: April 2, 2020, 14:56 »
In general, if you have a cif-file in your project folder, it should then appear in the QuantumATK NanoLab GUI. After selecting this cif-file in the GUI, a configuration object appear on the LabFloor. This object can then be drag-and-dropped on the text Editor available in the GUI and the corresponding file can be saved as a python file. See also this https://docs.quantumatk.com/tutorials/quantumatk_io_import/quantumatk_io_import.html for other options.