Recent Posts

1

General discussions (Q&As) / Re: Setting up 3D-DART with X3DNA

« Last post by spita on December 30, 2025, 02:15:24 pm »

Thanks for sharing, Dr. Jun.
 I have downloaded the files, and I'll try to use this version with 3D-DART.
Kind regards.

2

General discussions (Q&As) / Re: Setting up 3D-DART with X3DNA

« Last post by xiangjun on December 30, 2025, 12:37:31 pm »

Hi

I'd like to run some DNA simulations employing 3D-DART and I faced this same issue in my Linux. Could I receive one x3DNA version 2.15 to test in my DNA sequence?

In the current context, I assume you are trying to download x3DNA v1.5 together with 3D-DART.

I have added links to the Downloads section for this specific version and its corresponding user manual. Once logged in, you should find the Downloads section at the top of the 3DNA Forum. Please let us know if you encounter any issues.

Best regards,

Xiang-Jun

3

General discussions (Q&As) / Re: Setting up 3D-DART with X3DNA

« Last post by spita on December 30, 2025, 11:26:12 am »

The attached file "x.out" has the following content:

handling file <struct_1_fixed.pdb>

Time used: 00:00:00:00
This structure has broken O3' to P[i+1] linkages
missing ' P  ' atom : residue name 'THY', chain B, number [  27 ]
missing ' OP1' atom : residue name 'THY', chain B, number [  27 ]
missing ' OP2' atom : residue name 'THY', chain B, number [  27 ]
missing ' P  ' atom : residue name 'THY', chain B, number [   1 ]
missing ' P  ' atom : residue name 'THY', chain B, number [  27 ]

This means 3DNA v2.4.4 itself is running properly.

However, the file also contains "EnergyPDNA.exe: command not found". EnergyPDNA.exe is not part of 3DNA, v1.5 or v2.x. It could be part of 3D-DART.

From 3DNA v1.5 to v2.x, there is indeed reorganization of data folders, including:

Code: [Select]

BASEPARS ---> config
Examples ---> examples
FIBER ---> fiber
The most important one is BASEPARS ---> config.

For your convenience, I have dug out 3DNA v1.5, and sent you an email with links for download.

Note that 3DNA v1.5 is no longer supported. Even 3DNA v2.x is under maintenance mode: no more new features, only bug fixes. All new developments are devoted to DSSR and SNAP, which supersede 3DNA.

Best regards,

Xiang-Jun

 I'd like to run some DNA simulations employing 3D-DART and I faced this same issue in my Linux. Could I receive one x3DNA version 2.15 to test in my DNA sequence?
Kind regards.

4

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« Last post by xiangjun on December 24, 2025, 10:58:53 am »

As a follow-up to my previous response, DSSR v2.7.1-2025dec22 checks the stereochemistry of sugar. For each L-sugar, the JSON output will contain the key/value: "is_L_sugar": true in the nts object.

For example, running the following DSSR command on PDB entry 4WB2:

Code: [Select]

x3dna-dssr -i=4wb2.pdb --json | jq '.nts[] | {nt_id, is_L_sugar}'
will generate the following JSON output (excerpt):

Code: [Select]

......
{
  "nt_id": "D.0G35",
  "is_L_sugar": true
}
{
  "nt_id": "D.0C36",
  "is_L_sugar": true
}
......

In version v2.7.0-2025dec09, DSSR checks for flipped base pairs relative to the backbone direction. In this aspect, the L-form shares the same topology as Z-DNA, and both are left-handed helices. In version v2.7.1-2025dec22, DSSR takes into account the stereochemistry of the sugar to clearly distinguish between L and Z-form DNAs based on their L- and D-sugar configurations.

In this process, DSSR has been enhanced in multiple areas like classification and rebuilding by incorporating the L-form into a comprehensive framework. I highly value user feedback because it provides new insights that I might otherwise overlook. Once I fully grasp an issue, it often leads to an improved version of DSSR.

Xiang-Jun

5

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« Last post by xiangjun on December 08, 2025, 11:36:31 pm »

Hi Di and Gengshi,

Thanks for bringing L-DNA to my attention. I've updated DSSR to v2.7.0-2025dec09, which automatically recognizes L-DNA/RNA steps. Using your model PDB (`b40-rb10.5_out_minimized_aligned2Z_i_x.pdb`) as an example, the new DSSR output is as follows:

Code: [Select]

  helix#1[1] bps=40
      strand-1 5'-AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGG-3'
       bp-type    ||||||||||||||||||||||||||||||||||||||||
      strand-2 3'-TTTTTTTTTTAAAAAAAAAAGGGGGGGGGGCCCCCCCCCC-5'
      helix-form  LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
I’ve also tested it on PDB entry 4wb2, using biological unit 1 in the file 4wb2.pdb1, and the following output was obtained:

Code: [Select]

  helix#1[3] bps=9
      strand-1 5'-gcgugugug-3'
       bp-type    |||||||||
      strand-2 3'-cgcacgcac-5'
      helix-form  LLxL.xLx

Since L-DNA isn't a common form and DSSR may require further improvements to handle it better, I haven’t updated the documentation or the note in the DSSR output yet. Please let me know if the new DSSR output makes sense to you and share any questions or suggestions. Future updates to this feature would be much faster than this initial implementation.

Best regards,

Xiang-Jun

6

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« Last post by xiangjun on November 18, 2025, 09:25:57 pm »

Hi Di and Gengshi,

Thanks for the additional information. They are exactly the kind of information I was looking for.

• Glen Report 33-21: L-DNA: Applications and the Recognition of Mirror Image Nucleic Acids
• Structural basis for the targeting of complement anaphylatoxin C5a using a mixed L-RNA/L-DNA aptamer (PDB entry 4WB3)

I'll study them carefully, and try to implement an option in DSSR to handle L-DNA atuomatically. I'll keep you updated.

Best regards,

Xiang-Jun

7

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« Last post by Di_Liu on November 18, 2025, 06:24:18 pm »

By the way, here is a pdb structure containing both L-DNA and L-RNA: https://www.rcsb.org/structure/4WB3

8

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« Last post by GengshiWu on November 18, 2025, 05:56:47 pm »

Thank you for the clarification!

9

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« Last post by Di_Liu on November 18, 2025, 04:05:42 pm »

Hi Xiang-Jun,

L-DNA is totally synthetic from the mirror-image sugar, but now is very widely used. Here is a brief intro from Glen: https://www.glenresearch.com/reports/gr33-21
Let me further clarify: reversing the x-coordinates is actually performing the reflection about the yz plane, which is a special case. More generally, L-DNA can be generated by performing the reflection about any plane.
Thanks for considering to handle L-DNA with DSSR! L-sugar could be readily determined from the chiral carbon atoms on the sugar.

Di

10

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« Last post by GengshiWu on November 18, 2025, 01:30:40 pm »

Xiang-Jun,

Thank you for considering an adding the L-DNA option in DSSR. And I think your summary captures exactly what I mean by L-DNA: a left-handed helix with B-like geometry and a smooth backbone, distinct from Z-DNA. At this moment, I don’t have additional L-DNA examples. But I’ll share more on the forum with the community as I'll need to generate and study them.

Best,
Gengshi Wu