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Questions and answers > General discussions (Q&As)
3DNA 2.4.3 Rebuild
xiangjun:
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: ---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
--- End code ---
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
Beñat Olave:
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.
xiangjun:
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
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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.
