Recent Posts

1

Site announcements / The 3DNA Forum Has Moved to GitHub Discussions (Forum Now Archived)

« Last post by xiangjun on Today at 12:53:26 am »

Dear 3DNA and DSSR Community,

Since December 2011, the 3DNA Forum has served as the central meeting place for users and developers of 3DNA, DSSR, and related nucleic acid structural tools. Over these 15 years, our community has grown to 5,918 members, generating 958 topics and 3,770 posts. Every question, bug report, and feature discussion shared here has helped refine the algorithms, improve documentation, and shape the software into what it is today. Maintaining this forum and interacting with researchers around the world has been an immensely rewarding experience.

As part of our NIH-funded modernization under the X3DNA-DSSR National Resource (grant R24GM153869), community discussions and user support have officially moved to GitHub Discussions:

👉 https://github.com/orgs/x3dna-dssr/discussions


Why We Are Moving
While this self-hosted SMF board has served us faithfully, modern web standards offer a far smoother experience:

• Instant Access without Registration Hassles: Most computational biologists and bioinformaticians already have a GitHub account. You no longer need to register a separate account or wait for manual admin verification.
  
• Reliable Email Notifications: Subscribe directly to threads and categories to receive instant email notifications when someone replies.
  
• Modern Formatting: Native GitHub-flavored Markdown, syntax-highlighted code blocks, inline LaTeX math equations, and drag-and-drop image/screenshot pasting.
  
• Unified Ecosystem: Centralized support spanning the entire toolchain—3DNA (v1.5 and v2.4), standalone DSSR, wDSSR, and dssr-pymol.
  

What Happens to This Forum?

• Permanent Read-Only Archive: All existing 958 topics, 3,770 posts, tutorials, and historical Q&As will remain permanently online and searchable at forum.x3dna.org. None of this valuable knowledge is going away.
  
• Posting & New Registrations Closed: To eliminate automated spam registrations and administrative overhead, new user sign-ups and new postings on this SMF board have been disabled.
  

Where to Go from Here

• Ask Questions & Get Support: GitHub Discussions (All Tools)
  
• wDSSR Web Interface: web.x3dna-dssr.org
  

Thank you to every member who has contributed a post, shared a dataset, or reported an edge case over the past decade and a half. We look forward to continuing the conversation in our new GitHub home!

Xiang-Jun

2

General discussions (Q&As) / Re: Questions about 3DNA

« Last post by xiangjun on October 19, 2026, 11:08:09 am »

Hi Abermebo,

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

You should now be able to access the Downloads page to download 3DNA v2.4. Regarding your specific question, please provide a concrete example so others can reproduce your problem.

Best regards,

Xiang-Jun

3

General discussions (Q&As) / Questions about 3DNA

« Last post by Abermebo on October 16, 2026, 04:04:10 am »

Dear Dr. Xiang-Jun Lu,

First, of all thank you for accepting me in the forum and for your work. Could you please tell me where I can download the 3DNA v2.4 to perform structural analysis of nucleic acids? (academic research)

I would also like to ask you a more specific question. I am analyzing a modified base pair (completely different from WC bp), and when trying to determine the base-step parameters using nastruct, I obtain some artifacts (especially in the twist) due to the structural flexibility of the pair. I belive the best option would be to use the so-called simple helical parameters, based on consecutive C1'-C1' vectors. However, the problem is how to make the program recognize these non-natural bases. Is there any way to force the program to recognize them?

Thank you very much in advance for your help 

4

RNA structures (DSSR) / Re: DSSR version compatibility with SAMPDI-3Dv2 (v2.4.5 required)

« Last post by xiangjun on October 02, 2026, 01:53:54 pm »

Hi Shengzhi Qian,

Thank you for your interest in DSSR.

Starting with v2.0, Columbia University manages DSSR licensing. Columbia Technology Ventures (CTV) is the exclusive distributor for DSSR licenses. Version 1.9.10-2020apr23 is the final release available without a CTV license.

DSSR features remain consistent with the documentation provided in the 2015 DSSR and 2020 DSSR-PyMOL publications in NAR. I am not affiliated with SAMPDI-3D. To determine reproducibility, you must test v1.9.10 locally or contact the SAMPDI-3D developers for technical specifications.

Best regards,

Xiang-Jun

5

RNA structures (DSSR) / DSSR version compatibility with SAMPDI-3Dv2 (v2.4.5 required)

« Last post by ShengzhiQian on October 02, 2026, 10:29:18 am »

Hi Xiang-Jun,

Thank you for approving my 3DNA Forum account.

I am currently trying to reproduce SAMPDI-3Dv2 locally. According to the SAMPDI-3Dv2 documentation, the original implementation used x3dna-dssr v2.4.5.

In the Downloads section of the 3DNA Forum, I found DSSR v1.9.10-2020apr23 for Linux, but I could not find v2.4.5.

Could you please advise whether DSSR v1.9.10 is compatible with SAMPDI-3Dv2, or whether an archived Linux version of DSSR v2.4.5 is still available?

Thank you very much for your help.

Best regards,
Shengzhi Qian

6

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

« Last post by xiangjun on September 17, 2026, 06:45:39 pm »

Hi All,

In DSSR v2.9.4, the classification of sugar pucker has been revised, as shown below:

Code: [Select]

  phase-angle: the phase angle of pseudorotation, and the sugar pucker it corresponds to
  sugar-type:  ~C2'-endo  -- Dp < 2.9 A and phase angle in [108, 216],
                             covering C1'-exo, C2'-endo, and C3'-exo
               ~C3'-endo  -- Dp >= 2.9 A and phase angle in [324, 360] or [0, 72],
                             covering C2'-exo, C3'-endo, and C4'-exo
               pucker-CHK -- Dp and phase-angle assignments disagree; worth inspecting
This procedure evaluates consistency between the Dp and pseudorotation phase-angle assignments, flagging discordant cases as pucker-CHK. For 3-terminal sugars, where Dp is undefined due to the absence of a downstream phosphate group, the assignment relies exclusively on the phase angle within the defined ∼C2'-endo ([108, 216]) and ∼C3'-endo ([324, 360] or [0, 72]) intervals.

See attached file 1BNA_L-torsions.txt, derived from 1BNA_L.pdb.

Best regards,

Xiang-Jun

7

RNA structures (DSSR) / Re: overlapping area calculation - stacking interactions

« Last post by xiangjun on September 04, 2026, 01:02:59 pm »

Hi Agnieszka,

The issue you reported should have been fixed by Shuxiang. Below is a part of the output from a user-uploaded PDB file on wDSSR.

Code: [Select]

****************************************************************************
Overlap area, in Angstrom^2, between polygons defined by atoms on successive
bases. Polygons projected in the mean plane of the associated base-pair step.

Values in parentheses measure the overlap of base ring atoms only. Those
outside parentheses include exocyclic atoms on the ring. Intra- and inter-
strand overlap is designated according to the following diagram:

                    i2  3'      5' j2
                       /|\      |
                        |       |
               Strand I |       | II
                        |       |
                        |       |
                        |      \|/
                    i1  5'      3' j1

     bp      i1-i2        i1-j2        j1-i2        j1-j2        sum
   1 G-C  6.90( 3.38)  0.00( 0.00)  0.00( 0.00)  0.96( 0.00)  7.86( 3.38)    # |1|A|G|3||||   |1|A|C|261|||| 19-XIX    cWW  cW-W  WC
   2 U-G  5.92( 2.45)  0.00( 0.00)  0.03( 0.00)  2.31( 1.07)  8.26( 3.52)    # |1|A|U|4||||   |1|A|G|107|||| 28-XXVIII cWW  cW-W  Wobble
   3 G-A  0.00( 0.00)  0.00( 0.00)  0.00( 0.00)  0.00( 0.00)  0.00( 0.00)    # |1|A|G|5||||   |1|A|A|260|||| --        cSW  cm-W  --
   4 U-A  0.00( 0.00)  0.39( 0.00)  0.00( 0.00)  1.27( 1.26)  1.66( 1.26)    # |1|A|U|24||||  |1|A|A|247|||| 20-XX     cWW  cW-W  WC
   5 C-G  0.15( 0.00)  0.00( 0.00)  0.00( 0.00)  3.26( 1.82)  3.41( 1.82)    # |1|A|C|23||||  |1|A|G|248|||| 19-XIX    cWW  cW-W  WC
   6 U-A  6.41( 3.40)  0.00( 0.00)  0.00( 0.00)  3.96( 2.40) 10.37( 5.80)    # |1|A|U|22||||  |1|A|A|249|||| 20-XX     cWW  cW-W  WC
......
Please let us know if you still see the problem, or any other issues related to DSSR or wDSSR.

Best regards,

Xiang-Jun

8

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

« Last post by JiaolongBao on August 27, 2026, 02:19:14 am »

Hi Xiang-Jun,

Thanks for the update. It is indeed a good way to distinguish C2'-endo and C3'-endo both in L-sugars and D-sugar circumstance. I believe the sugar-class classification in dssr-torsion.txt for 1BNA_L.pdb is correct.

Best regards,

Jiaolong

9

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

« Last post by xiangjun on August 25, 2026, 11:33:26 pm »

Hi Jiaolong,

As a follow-up to your July 06, 2026 post:

The sugar class classification for L-sugar is omitted due to some compatibility reason with D-sugar.

As of v2.9.3-2026aug26, DSSR employs ssZp to classify L-sugars and D-sugars into C2'-endo or C3'-endo conformations. Below are related excerpts from the dssr-torsions.txt output file:

  phase-angle: the phase angle of pseudorotation and puckering
  sugar-type: ~C2'-endo for C2'-endo like conformation (|ssZp| <= 2.5 A), or
               ~C3'-endo for C3'-endo like conformation (|ssZp| >= 3.3 A)
              Note the ONE column offset (for easy visual distinction)

ssZp: single-stranded Zp, defined as the z-coordinate of the 3' phosphorus atom
      (P) expressed in the standard reference frame of the 5' base; the value is
      POSITIVE when P lies on the +z-axis side (base in anti conformation);
      NEGATIVE if P is on the -z-axis side (base in syn conformation)
  Dp: perpendicular distance of the 3' P atom to the glycosidic bond
      [Ref: Chen et al. (2010): "MolProbity: all-atom structure
            validation for macromolecular crystallography."
            Acta Crystallogr D Biol Crystallogr, 66(1):12-21]

Attached is an example DSSR run on 1BNA_L.pdb (1BNA.pdb with negated x-coordinates: xL=-x) and the related dssr-torsions.txt file.

Best regards,

Xiang-Jun

10

RNA structures (DSSR) / Re: overlapping area calculation - stacking interactions

« Last post by shuxiang on August 25, 2026, 10:09:46 am »

Hi Agnieszka,

The wDSSR server has been updated with overlapping area calculations for the user-uploaded structures. Thanks.

Best,
Shuxiang