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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 :)
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Please provide more details, preferably with screenshots.
Thanks,
Xiang-Jun
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Hello, this is an example:
(https://serving.photos.photobox.com/95871559491ca187e95093ac8876c97286410561a4f184eabab1d88fc20b752a2605be53.jpg)
(https://serving.photos.photobox.com/69096671a4945eec73b4a228faef9616c06d143cf88d1a0c1853a6b55446355f94f3416b.jpg)
(https://serving.photos.photobox.com/921592945e2686bc774eefaa529fddcd8f8640c6546f6cfc5e88cc2bc115cdc5b1bf8239.jpg)
(https://serving.photos.photobox.com/0290775823fb9a540a09b408ab126adce036dc2104f897af51345129f30717a2855afe56.jpg)
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Thanks for the screenshots.
Could you please translate the error message of x3dna_utils into English?
Xiang-Jun
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Yes, sorry, it says:
"is not recognized as an internal or external command, operable program or batch file"
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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:
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
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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.
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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
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