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Author Topic: 3DNA 2.4.3 Rebuild  (Read 16307 times)

Offline Beñat Olave

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3DNA 2.4.3 Rebuild
« on: November 06, 2018, 01:11:05 pm »
Hello,

I wanted to rebuild the DNA with backbone included but typing "cp_std" before adding rebuild command is not working, neither typing "x3dna_utils cp_std" as shown in help. They are not recognized as commands.

I would appreciate a possible solution  :)

Offline xiangjun

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Re: 3DNA 2.4.3 Rebuild
« Reply #1 on: November 06, 2018, 01:25:21 pm »
Please provide more details, preferably with screenshots.

Thanks,

Xiang-Jun

Offline Beñat Olave

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Re: 3DNA 2.4.3 Rebuild
« Reply #2 on: November 06, 2018, 02:04:47 pm »
Hello, this is an example:








Offline xiangjun

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Re: 3DNA 2.4.3 Rebuild
« Reply #3 on: November 06, 2018, 02:16:01 pm »
Thanks for the screenshots.

Could you please translate the error message of x3dna_utils into English?

Xiang-Jun

Offline Beñat Olave

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Re: 3DNA 2.4.3 Rebuild
« Reply #4 on: November 06, 2018, 02:19:36 pm »
Yes, sorry, it says:

"is not recognized as an internal or external command, operable program or batch file"

Offline xiangjun

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Re: 3DNA 2.4.3 Rebuild
« Reply #5 on: November 06, 2018, 02:47:54 pm »
Got it -- thanks.

The error message is due to a limitation with Windows command environment. The x3dna_utils Ruby script is not recognized in native Windows. You may consider installing MSYS2 which is more flexible and much Linux-like.

Or, you could simply run the following commands in your working directory:

Code: [Select]
copy %X3DNA%\config\atomic\BDNA_A.pdb Atomic_A.pdb
copy %X3DNA%\config\atomic\BDNA_C.pdb Atomic_C.pdb
copy %X3DNA%\config\atomic\BDNA_G.pdb Atomic_G.pdb
copy %X3DNA%\config\atomic\BDNA_T.pdb Atomic_T.pdb
copy %X3DNA%\config\atomic\BDNA_U.pdb Atomic_U.pdb

You may need to adjust with the 'config' part due to your settings. Then you'll be able to build a DNA structure with B-form backbone. Have a try and report back how it goes.

Xiang-Jun



Offline Beñat Olave

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Re: 3DNA 2.4.3 Rebuild
« Reply #6 on: November 06, 2018, 07:15:06 pm »
Hello, I made it copying and renaming the files, I still have to elucidate how to use MSYS2, as soon as I do I will post it.

Best regards.

Offline xiangjun

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Re: 3DNA 2.4.3 Rebuild
« Reply #7 on: November 06, 2018, 07:29:56 pm »
After copying in the files in ConEmu, please re-run the rebuild program with the -atomic option as in your screenshot. You'll see your rebuilt structure with B-form backbone atoms.

Installing MSYS2 is a separate issue. I strongly suggest you, or any 3DNA user on Windows, do so since it makes using 3DNA (a command-line tool) so much easier.

Best regards,

Xiang-Jun

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.