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Author Topic: How to set up 3DNA on Windows with WSL2  (Read 706 times)

Offline nat520

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How to set up 3DNA on Windows with WSL2
« on: December 14, 2024, 06:47:13 am »
Dear Dr. Lu,

I am trying to install x3dna-v2.4 on Windows 11 following the instructions.
However, I still can't execute find_pair -h on ConEmu.
I tried to perform some troubleshooting by looking over similar issues posted on this forum, such as "dir", "echo %X3DNA%", "echo %PATH%" and "dir %X3DNA%config\version".. and all the feedbacks seem alright..
I actually have tried Ruby and Mingw too but that all still didn't work out so in the end i got rid of them.
I have attached the screenshots, can you help on this, where have I missed out?
And I would like to get a confirmation that x3dna-v2.4 does not need a license to download, and working on native window using ConEmu is perfectly alright?

Kind Regards,
Chian



Offline xiangjun

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Re: How to set up 3DNA on Windows with WSL2
« Reply #1 on: December 14, 2024, 08:41:59 am »
Hi Chian,

Thanks for using 3DNA. Working in native Windows command-line (cmd or PowerShell) has seen lots of troubles, as evidenced from this long thread. I've split the thread so it is easier to see the new posts.

Since you are on Windows 11, please install WSL2 (Window Subsystem for Windows). The default ubuntu system is good to get 3DNA up and running quickly. Please have a try and report back how it goes.

Xiang-Jun
« Last Edit: December 14, 2024, 09:17:29 am by xiangjun »

Offline nat520

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Re: How to set up 3DNA on Windows with WSL2
« Reply #2 on: December 14, 2024, 10:17:54 am »
Dear Dr. Lu,

I am onboard!!!

I have actually set up WSL on my laptop a very long time ago. So I've saved all the installation parts for the WSL2.

I installed the tarball file named x3dna-v2.4-linux-64bit.tar.gz. and moved it to the home directory for my WSL linux.

Then I opened up the WSL2 command prompt and followed the download instructions for linux.

I installed ruby by entering "sudo apt install ruby" in the WSL linux command prompt, but encountered some issues regarding error 404, but it was because my WSL was out of date. This was easily solved by "sudo apt update", followed by repeating the "sudo apt install ruby".

I then continue the download instructions, set up the environment variable X3DNA and add $X3DNA/bin to my command search path.

And finally, find_pair-h works!

Thanks for your prompt reply and suggestion on using WSL2 for running this program! I can start exploring the features and functions of 3DNA whilst waiting for the DSSR license to come through!

Kind Regards,
Chian

 

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University