Recent Posts

1

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

« Last post by xiangjun on Today at 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

2

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 

3

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

4

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

5

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

6

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

7

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

8

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

9

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

10

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

« Last post by xiangjun on August 25, 2026, 09:51:06 am »

Hi Agnieszka,

Thanks for reporting this issue. I was able to reproduce it and can confirm that it happens on my end as well. The pre-processed PDB files have the option specified for overlapping area calculation, but the script processing user-uploaded files does not. I have notified Shuxiang (who recently joined our team) about this. It should be fixed soon, and we will let you know once it is resolved.

Best regards,

Xiang-Jun