Messages

1

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

« 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

2

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

« 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

3

FAQs / Re: Where to download x3DNA

« on: August 16, 2026, 11:38:51 pm »

Hi,

The issue should be fixed now. It was due to my negligence.

Best regards.

Xiang-Jun

4

General discussions (Q&As) / Re: Could you tell me where l can download 3DNA?

« on: July 24, 2026, 09:16:16 am »

Hi Gai,

You should now be able to see the Download link in the top of the Forum.

Because you registered with a personal email address, it is difficult to verify your account and filter out spam. By default, new unverified accounts are assigned to a restricted category where the Download link is hidden and posts are moderated. This policy prevents spam and ensures the Forum remains clean and trustworthy.

Best regards,

Xiang-Jun

5

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

« on: July 10, 2026, 01:34:37 pm »

Hi Jiaolong,

Thank you for providing the technical details and verification of the DSSR implementation for the classification of L-sugars. Detailed responses like this help improve the software and set a standard for community interaction.

I compiled four examples based on the information you provided to illustrate how the signs of the base-pair parameters are defined. See the Practical Guide associated with the 2020 DSSR-PyMOL paper for details. The base blocks and the standard base-reference frame attached to each base clarify the sign convention of base-pair and step parameters. PyMOL session files are attached so users can easily verify the results.

DSSR is under active development, and community interactions improve the software. I address questions and bug reports quickly. Users are encouraged to seek clarification regarding execution errors or unsupported features on the forum for their own benefit and that of the community as a whole.

Best regards,

Xiang-Jun

6

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

« on: June 17, 2026, 06:50:45 am »

Hi Jiaolong,

Thanks for the detailed explanation—this kind of feedback is exactly what I have been looking for.

I will certainly investigate the sign convention further. In this post, I would like to address the sugar-class issue. Currently, the L-sugar class is determined based on the pseudorotation phase angle, using the exact same criteria as for D-sugars. I have attached the dssr-torsions.txt output for 1BNA_L.pdb. Honestly, I had not paid close attention to this specific aspect of L-DNA before. Please let me know the correct way to determine the sugar class in these cases.

For this type of discussion, a phone call or a video meeting might be more convenient. Please let me know if you would like to connect online or over the line to discuss this topic further.

Best regards,

Xiang-Jun

7

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

« on: June 16, 2026, 08:30:02 am »

Hi JiaolongBao,

Thank you for your follow-up on this topic. The analysis of L-DNA (with mirror-image sugar-phosphate backbones) is a new DSSR feature, added in response to user requests. DSSR can identify the mirror-image sugar components and classify the corresponding steps as L-DNA with a negative twist angle. Running DSSR on your 1BNA_L.pdb file yields the following results:

Code: [Select]

# x3dna-dssr -i=1BNA_L.pdb --more
  helix#1[1] bps=12
      strand-1 5'-CGCGAATTCGCG-3'
       bp-type    ||||||||||||
      strand-2 3'-GCGCTTAAGCGC-5'
      helix-form  LLLLLLLLLLL
    helical-rise:   3.35(0.44)
    helical-radius: 9.37(0.98)
    helical-axis:    0.088    -0.275    -0.958
       point-one:  -16.795    25.817    26.180
       point-two:  -13.557    15.707    -9.067
   1 A.DC1          B.DG24         C-G WC           19-XIX    cWW  cW-W
        bp1-pars:* [-0.42    -0.27    -0.06    -2.76    14.18    -3.67]
       step-pars:  [0.36     0.15     3.52     -3.40    -6.44    -40.31]
       heli-pars:  [0.55     0.11     3.52     9.26     -4.88    -40.94]
        bp2-pars:* [-0.02    -0.27    -0.25    4.45     10.83    -4.02]
       C1'-based:                rise=3.52                 twist=-38.57
       C1'-based:              h-rise=3.52               h-twist=-39.23
...

Regarding the sign inversion pattern of the base-pair and step/helical parameters, you are the first user to raise this question. In the current implementation, certain base-pair parameters are reversed due to the adjustment of the base reference frame, and the corresponding step/helical parameters follow those adjustments. I will examine the source code details and follow up on this topic soon.

From a user perspective, what behavior do you consider most logical? As the DSSR developer, I want the tool to meet user expectations while remaining mathematically consistent. The current implementation satisfies the requirements of Di and Gengshi, who initially requested this feature.

Best regards,

Xiang-Jun

8

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

« on: June 08, 2026, 10:09:05 am »

Hi Agnieszka,

wDSSR has been updated with overlapping area calculation for 3DNA output. See 355d for an example.

Please let me know if you have any questions.

Best regards,

Xiang-Jun

9

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

« on: June 03, 2026, 11:37:00 am »

Hi Agnieszka,

Thank you for using 3DNA/DSSR and for sharing your feedback.

The new wDSSR website introduces several modernized features, though a few specialized analyses from the legacy 3DNA 2.0 web server were initially omitted to keep the interface streamlined. Based on recent user requests, we have already restored backbone torsion angles to the wDSSR platform.

Regarding the base-pair overlapping area: this metric is calculated by the underlying DSSR engine but is not yet rendered on the wDSSR web server. In the meantime, you can obtain these overlapping areas directly by running the DSSR command-line program locally.

We are happy to integrate this feature into the web platform. Which format would best fit your workflow? For instance, would adding a dedicated section to the downloadable wDSSR output file be sufficient?

Code: [Select]

Overlap area in Angstrom^2 between polygons defined by atoms on successive
bases. Polygons projected in the mean plane of the designed 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

     step      i1-i2        i1-j2        j1-i2        j1-j2        sum
   1 CG/CG  1.48( 0.00)  0.00( 0.00)  0.97( 0.00)  0.94( 0.00)  3.39( 0.00)
   2 GC/GC  2.95( 0.63)  0.00( 0.00)  0.00( 0.00)  0.96( 0.04)  3.91( 0.68)
   3 CG/CG  2.66( 0.00)  0.00( 0.00)  0.15( 0.00)  3.44( 0.21)  6.25( 0.21)
   4 GA/TC  3.94( 1.11)  0.00( 0.00)  0.00( 0.00)  4.17( 0.78)  8.11( 1.88)
   5 AA/TT  3.51( 2.16)  0.00( 0.00)  0.00( 0.00)  5.09( 0.08)  8.60( 2.24)
   6 AT/AT  5.91( 2.14)  0.00( 0.00)  0.00( 0.00)  5.65( 1.89) 11.56( 4.03)
   7 TT/AA  5.08( 0.11)  0.00( 0.00)  0.00( 0.00)  3.68( 2.39)  8.76( 2.51)
   8 TC/GA  2.20( 0.00)  0.00( 0.00)  0.00( 0.00)  4.98( 2.19)  7.18( 2.19)
   9 CG/CG  5.50( 1.17)  0.00( 0.00)  0.01( 0.00)  1.56( 0.00)  7.06( 1.17)
  10 GC/GC  0.57( 0.00)  0.00( 0.00)  0.00( 0.00)  5.32( 2.35)  5.89( 2.35)
  11 CG/CG  0.73( 0.00)  0.00( 0.00)  0.54( 0.00)  1.98( 0.03)  3.25( 0.03)
Best regards,

Xiang-Jun

10

Feature requests / Re: where are the torsion angles?

« on: June 01, 2026, 10:54:40 pm »

As a follow up, the wDSSR web server has been updated to include a link to torsion angles in the "Analyze" module. See an example output for PDB entry 1msy.

11

Feature requests / Re: where are the torsion angles?

« on: May 28, 2026, 10:25:56 pm »

Hi,

Thank you for your question. DSSR calculates a wide range of structural features, including backbone torsion angles. To keep the initial release of the wDSSR web server streamlined and accessible, some of these detailed parameters were intentionally omitted from the default display. In the meantime, you can obtain complete torsion angle profiles using the DSSR command-line tool, as detailed in the DSSR User Manual.

We can update wDSSR to make this data available on the web interface. Would you prefer to have the torsion angles included in a downloadable JSON output file, or displayed explicitly in a new section on the results page?

Best regards,

Xiang-Jun

12

FAQs / Re: Where to download x3DNA

« on: May 11, 2026, 05:09:54 pm »

Hi,

Thank you for joining the 3DNA/DSSR community. For security, initial posts from non-EDU addresses require a one-time approval. This has been completed, and your download link is now active.

Best regards,

Xiang-Jun

13

FAQs / Re: Where to download x3DNA

« on: April 27, 2026, 10:24:39 am »

Hi Changdong,

Thank you for the follow-up.

I would like to clarify that the licensing for DSSR is managed by Columbia Technology Ventures (CTVs). While DSSR has a large global community with hundreds of academic users, licenses are generally not issued to institutions in certain countries due to institutional compliance and administrative policies. Unfortunately, this means that even if an academic request is submitted, it may be restricted based on the location of the host institution.

However, you can still access DSSR through the following options:

• DSSR v1.9.10-2020apr23: This version is available for download directly from the 3DNA Forum. It corresponds to the paper "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL" (2020) published in Nucleic Acids Research.
• wDSSR: You can use the recently released web interface for DSSR at https://web.x3dna-dssr.org/.
  

I appreciate your interest in the software and your understanding of these constraints.

Best regards,

Xiang-Jun

14

FAQs / Re: Where to download x3DNA

« on: April 24, 2026, 07:22:52 am »

Hi Changdong,

Thanks for your interest in 3DNA/DSSR. Your question has been addressed in another thread: License requested.

Please don’t hesitate to ask questions on the forum, but kindly avoid posting the same query in multiple threads to keep the discussion organized.

Best regards,

Xiang-Jun

15

RNA structures (DSSR) / Re: License requested

« on: April 24, 2026, 07:13:13 am »

Hi Changdong,

Thanks for reaching out. You should now be able to see the Download link at the very top of the forum.

Due to a high volume of spam, I have implemented a filter for registered users. Although your account was created in 2018, it remained in a "Pending" category because you had not yet posted on the 3DNA Forum. Once a user's first post is approved, the Download link becomes visible automatically.

Best regards,

Xiang-Jun

16

Bug reports / Re: Missing DNA bases with negative residue number

« on: April 14, 2026, 02:12:50 pm »

Hi Mihir,

Great catch! I have successfully reproduced the issue. The bug is due to a parsing error within the wDSSR web interface. As shown below, the core DSSR engine itself handles negative residue numbering without any issues.

Execute the following command to see the enumeration:

Code: [Select]

x3dna-dssr mutate -i=9GBV.pdb --enum
An excerpt of the output is as follows:

# For each entry to be mutated, remove the leading #, and add to=base

# To mutate A.A9 to G in PDB entry 1ehz (tRNA):
#          #  chain=A name=A num=9  #9  A.A9
#       --->  chain=A name=A num=9 to=G

# To mutate B.DT19 to DC in PDB entry 355d (B-DNA):
#          #  chain=B name=DT num=19  #19  B.DT19, pairedNt=A.DA6
#       --->  chain=B name=DT num=19 to=DC

# Empty or comment (starting with #) lines are ignored.

#  chain=E name=DT num=-37  #1  E.DT-37, pairedNt=F.DA80
#  chain=E name=DG num=-36  #2  E.DG-36, pairedNt=F.DC79
#  chain=E name=DC num=-35  #3  E.DC-35, pairedNt=F.DG78
#  chain=E name=DC num=-34  #4  E.DC-34, pairedNt=F.DG77
#  chain=E name=DA num=-33  #5  E.DA-33, pairedNt=F.DT76
#  chain=E name=DT num=-32  #6  E.DT-32, pairedNt=F.DA75
#  chain=E name=DC num=-31  #7  E.DC-31, pairedNt=F.DG74
#  chain=E name=DA num=-30  #8  E.DA-30, pairedNt=F.DT73
#  chain=E name=DG num=-29  #9  E.DG-29, pairedNt=F.DC72
#  chain=E name=DA num=-28  #10  E.DA-28, pairedNt=F.DT71
#  chain=E name=DA num=-27  #11  E.DA-27, pairedNt=F.DT70
#  chain=E name=DA num=-26  #12  E.DA-26, pairedNt=F.DT69
#  chain=E name=DA num=-25  #13  E.DA-25, pairedNt=F.DT68
#  chain=E name=DC num=-24  #14  E.DC-24, pairedNt=F.DG67
......

We will resolve this wDSSR error shortly. In the meantime, please continue using the tool and report any further issues you encounter.

If it is an option for your workflow, I recommend installing the standalone version of DSSR on your computer and using the command-line interface directly.

Best regards,

Xiang-Jun

17

Bug reports / Re: Missing DNA bases with negative residue number

« on: April 14, 2026, 11:34:06 am »

Hi,

Thank you for using our tools and for reaching out on the forum.

To help us investigate this further, could you please provide a step-by-step description of your workflow? Specifically, please include the exact commands or options you used so that we can reproduce the issue on our end. This will help us determine why the residues with negative numbers are not being displayed as expected.

Best regards,

Xiang-Jun

18

General discussions (Q&As) / Re: Approach for building G-quadruplex models with 3'-3' and 5'-5'polarity inversion

« on: April 06, 2026, 02:02:29 pm »

Hi muha,

Thanks for posting on the Forum, and sorry for the late reply.

I understand your aim to build a unimolecular G-quadruplex model with alternating 5'-3', 3'-3', 3'-5', and 5'-5' linkages. DSSR does not have a built-in option for building such models, and I am not aware of any other software that can do this. In my understanding, this would require a combination of DSSR and a 3D manual editing tool to adjust the polarity of the linkages.

As far as analysis is concerned, DSSR should be able to identify G-tetrads, and may take each tract as broken chains. We need specific examples to show how DSSR should behave in these cases. I will consider modifying DSSR to handle these cases if feasible.

Best regards,

Xiang-Jun

19

FAQs / Re: Where to download x3DNA

« on: April 01, 2026, 03:03:00 pm »

Hi Luca,

Thanks for your interest in 3DNA. You should now be able to see the download page on the 3DNA Forum.

Best regards,

Xiang-Jun

20

Site announcements / Staff Associate II (Computational Structural Biology) at Columbia University

« on: April 01, 2026, 01:36:23 pm »

The X3DNA-DSSR resource is at the forefront of structural bioinformatics, developing advanced tools for analyzing and modeling nucleic acid structures. We are seeking a highly motivated Staff Associate II to join our team and contribute to our next-generation analysis and visualization engine.

To see our resource in action, please visit wDSSR, our new web interface for dissecting and modeling 3D nucleic acid structures: https://web.x3dna-dssr.org/.

We are looking for a candidate with a strong scientific background in structural biology or bioinformatics and a desire to contribute to peer-reviewed publications through community-driven data analysis. We value individuals who are eager to learn, adapt to new technical challenges, and support the global research community.

For the full job description and to submit your application, please visit the official Columbia University posting:
https://apply.interfolio.com/183705

21

Site announcements / Announcing wDSSR: The Next-Generation Web Interface to X3DNA-DSSR

« on: March 17, 2026, 05:30:52 pm »

Dear 3DNA/DSSR Community,

We are thrilled to announce the official launch of wDSSR (https://web.x3dna-dssr.org/), the powerful new web interface to the X3DNA-DSSR analytical engine.

Developed by Drs. Shuxiang Li and Xiang-Jun Lu and supported by NIH grant R24GM153869, wDSSR represents a major leap forward from our highly popular 2019 Web 3DNA 2.0 framework. While Web 3DNA 2.0 has faithfully served the community for the analysis, visualization, and modeling of 3D nucleic acid structures, wDSSR was built from the ground up to take full advantage of modern web technologies and the latest DSSR backend capabilities.

A Modern, Streamlined Scientific Workflow
We have completely overhauled the user interface to provide a clean, intuitive, and task-driven experience. The core modeling and analysis tools are now seamlessly organized into a logical, single-word scientific workflow: Analyze, Rebuild, Model, Circularize, Mutate, Assemble, and Visualize.

Spotlight Feature: The "Assemble" Module
One of the most exciting upgrades is the newly renamed Assemble tab (formerly "Composite"). This advanced composite model builder allows you to effortlessly construct complex, higher-order models by linking any combination of nucleic acid duplexes or protein-DNA/RNA complexes. You can quickly connect up to six distinct target structures, ranging from simple linked A-DNA and B-DNA duplexes to large, protein-decorated structural assemblies.

Immediate Global Adoption
Although wDSSR has just launched, we are incredibly humbled to share that it is already seeing rapid worldwide adoption! According to recent network infrastructure data, the new interface is actively being used by researchers across North America, South America, Europe, and Asia. Within just a few days, we have recorded active sessions from prestigious institutions around the globe, including:

• The Weizmann Institute of Science in Israel
• Katholieke Universiteit Leuven in Belgium
• Queen's University in Canada
• Universidad Nacional Autonoma de Mexico (UNAM) in Mexico
• Emory University and the Wadsworth Centers Laboratories and Research in the United States
• Jawaharlal Nehru University and the China Education and Research Network in Asia

How to Cite
While a dedicated paper for wDSSR is currently in preparation, researchers should cite the server using its URL (https://web.x3dna-dssr.org/) alongside the 2019 Web 3DNA 2.0 paper and the foundational 2015 DSSR paper. Full details and funding acknowledgements can be found on our newly consolidated About page.

We invite you all to try out the new wDSSR platform! As always, your feedback is invaluable to us, and we encourage you to share your thoughts, questions, and structural models via the newly updated Questions & Feedback link in the wDSSR footer.

Happy modeling!

22

FAQs / Re: Where to download x3DNA

« 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

23

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

« 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

24

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

« 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

25

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

« 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