3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: Beñat Olave on November 06, 2018, 01:11:05 pm

Title: 3DNA 2.4.3 Rebuild
Post by: Beñat Olave 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 :)
Title: Re: 3DNA 2.4.3 Rebuild
Post by: xiangjun on November 06, 2018, 01:25:21 pm: Please provide more details, preferably with screenshots.

Thanks,

Xiang-Jun
Title: Re: 3DNA 2.4.3 Rebuild
Post by: Beñat Olave on November 06, 2018, 02:04:47 pm: 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)
Title: Re: 3DNA 2.4.3 Rebuild
Post by: xiangjun 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
Title: Re: 3DNA 2.4.3 Rebuild
Post by: Beñat Olave 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"
Title: Re: 3DNA 2.4.3 Rebuild
Post by: xiangjun 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
Title: Re: 3DNA 2.4.3 Rebuild
Post by: Beñat Olave 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.
Title: Re: 3DNA 2.4.3 Rebuild
Post by: xiangjun 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