3DNA 2.4.3 Rebuild

[Beñat Olave]

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 

[xiangjun]

Please provide more details, preferably with screenshots.

Thanks,

Xiang-Jun

[Beñat Olave]

Hello, this is an example:

[xiangjun]

Thanks for the screenshots.

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

Xiang-Jun

[Beñat Olave]

Yes, sorry, it says:

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

[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: [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

[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