Recent Posts

1

FAQs / Re: Where to download x3DNA

« Last post by xiangjun on February 19, 2026, 09:29:26 am »

Hi Luca,

You should now have access to the Downloads section. To prevent spam, we manually monitor and verify all new registrations. This is a one-time process; now that you are verified, you can download the 3DNA software and post questions here in the forum.

Best regards,

Xiang-Jun

2

FAQs / Re: Where to download x3DNA

« Last post by Luca_Maggi on February 19, 2026, 03:33:57 am »

Hello!

Same here! I have received the e-mail confirming the registration but still don't see the download section.
Could you please give me access to that.

Many Thanks

Luca

3

General discussions (Q&As) / MOVED: Looking for a way to speed up do_x3dna process.

« Last post by xiangjun on February 15, 2026, 11:16:07 pm »

This topic has been moved to MD simulations.

http://forum.x3dna.org/index.php?topic=1060.0

4

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

5

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 

6

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

7

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

8

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

9

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

10

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.