Recent Posts

21

MD simulations / Re: Looking for a way to speed up do_x3dna process.

« Last post by xiangjun on February 15, 2026, 11:15:42 pm »

Hi Karn,

Thanks for posting on the 3DNA Forum. Since you are using do_x3dna, Dr. Kumar (@rkumar) is the best person to answer your question. I've move this thread to MD simulations section which is more relevant to MD simulations. Hopefully, he will chime in soon.

Best regards,

Xiang-Jun

22

MD simulations / Looking for a way to speed up do_x3dna process.

« Last post by Karn4132 on February 15, 2026, 12:12:04 pm »

Hello,

I'm a new user of do_x3dna and I've been trying to find the helical parameters of the damaged DNA - Protein complex.
I found the issue that sometimes - x3dna does not detect the damaged bp, so I tried adding -ref at the end of the command.|

do_x3dna -f ../new.xtc -s ../new.pdb -ref

Currently, this line of command seems to work perfectly.
However, by using the referrence structure for the calculation, it takes much longer than before to finish the process.

Is this a normal outcome for not using the base pair parameter of the trajectory?
It is worth to mention that my trajectory is pretty long and the old process actually took quite a while to finish. The new code made the calculation even longer than I expected.

Karn 

23

MD simulations / Re: Clarification on how DNA radius is computed from 3DNA/DSSR

« Last post by xiangjun on February 03, 2026, 09:25:43 am »

Hi Mamta,

Thanks for using 3DNA and for posting your question on the 3DNA Forum.

3DNA performs a least-squares fit of linear global helical axes using equivalent C1' and RN9/YN1 atom pairs along each strand of a DNA duplex. It then calculates mean and deviation of helix radius based on P, O4', and C1' atoms. Of course, the linear global helical axes is only meaningful when the DNA duplex is not strongly distorted. You may also want to check Curves+ for deriving curvilinear helical axes.

Using 355d as an example, running 3DNA as below:

find_pair 355d.pdb | analyze

You will get an output file 355d.out, which contains the following content:

Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 3.30(0.52)
Helix:    -0.1269   -0.2753   -0.9530
HETATM 9998  XS    X X 999      17.536  25.713  25.665
HETATM 9999  XE    X X 999      12.911  15.677  -9.080
Average and standard deviation of helix radius:
      P: 9.42(0.82), O4': 6.37(0.85),  C1': 5.85(0.86)

You can extract the two HETATM lines into the original PDB file, and draw a line between them to visualize the global helical axis (in PyMOL, for example).

The underling algorithm is based on the NewHelix/FreeHelix program, and you can check the implementation details in the 3DNA source code.

Hope this helps.

Best regards,

Xiang-Jun

24

MD simulations / Clarification on how DNA radius is computed from 3DNA/DSSR

« Last post by Mamta on February 03, 2026, 08:21:48 am »

Dear Xiang-Jun,
I am using 3DNA to analyze DNA structures from molecular-dynamics simulations.
I get the standard 3DNA output files with base-pair and helical axis information.

I want to calculate the DNA radius from these 3DNA results.
Could you please tell me:

Which output values or parameters from 3DNA should be used to compute the DNA radius, and how exactly should it be calculated from the 3DNA analysis?

Thank you.

Best regards,
Mamta Yadav

25

FAQs / Re: Where to download x3DNA

« Last post by xiangjun on January 11, 2026, 08:01:28 pm »

Hi,

You should now be able to see the Download section. Note that the current version of DSSR is distributed by the Columbia Technology Ventures (CTV).


Thanks for your interested in 3DNA/DSSR. If you have any questions, please do not hesitate to post them on the Forum.

Best regards,

Xiang-Jun

26

FAQs / Re: Where to download x3DNA

« Last post by jessex on January 11, 2026, 06:54:24 pm »

Hello,

I am also registered, but I do not see the download section.

Thank you

27

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.

28

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

29

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.

30

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