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21

RNA structures (DSSR) / Re: Question about axis tilt after reconstruction of B-DNA using x3dna-dssr

« Last post by GengshiWu on August 03, 2025, 07:37:32 pm »

Hi Xiang-Jun,

Thank you for your response!

22

RNA structures (DSSR) / Re: Question about axis tilt after reconstruction of B-DNA using x3dna-dssr

« Last post by xiangjun on August 01, 2025, 09:03:27 pm »

Is there a way to directly generate a -fiber DNA helix with 10.5 bp/turn aligned to the Z-axis, avoiding parameter extraction and rebuilding?

The fiber model is based on experimental data, the details can be found via the following command: x3dna-dssr fiber --list

So the answer is NO with 3DNA/DSSR.

Best regards,

Xiang-Jun

23

RNA structures (DSSR) / Re: Question about axis tilt after reconstruction of B-DNA using x3dna-dssr

« Last post by GengshiWu on August 01, 2025, 08:41:06 pm »

Hi Xiangjun,

Thank you for your explanation of the tilt in the rebuilt model,

To clarify our question, we extract parameters and rebuild because the B-DNA model generated with -fiber has 10 bp/turn, but we want a 10.5 bp/turn helix. To make it 10.5 bp/turn, we modify all twist values (except the last row) in dssr-B-DNA-A36-step.txt to 34.2857 (360°/10.5) before rebuilding.

Our goal is for the 10.5 bp/turn helix to align perfectly with the Z-axis, like the original fiber model. But as you noted, rebuilding positions the structure relative to its first base pair, causing some tilt.

Is there a way to directly generate a -fiber DNA helix with 10.5 bp/turn aligned to the Z-axis, avoiding parameter extraction and rebuilding?

24

RNA structures (DSSR) / Re: Question about axis tilt after reconstruction of B-DNA using x3dna-dssr

« Last post by xiangjun on August 01, 2025, 11:47:34 am »

Hi Gengshi,

Thanks for using DSSR and for posting your well-formulated question on the 3DNA Forum.

Could you please advise whether this tilt is expected due to reconstruction? Or is there a recommended way to maintain the original axis alignment during rebuilding?

Yes, the rebuilt structure and the original structure are in different coordinate systems, as expected. More specifically, the rebuilt structure is in the reference frame of the first base pair, while the original structure is in a whatever coordinate system it was originally in. For the fiber models from 3DNA/DSSR, base pairs grow from top to bottom, with decreasing z-coordinates. You can easily see this by looking at the dssr-B-DNA-A36.pdb file.

To put the two structures in the same coordinate system, you can use the --frame option of DSSR. Using your example, the command would be:

Code: Bash

1. # dssr-B-DNA-A36.pdb is the coordinate file from DSSR fiber model
2. x3dna-dssr -i=dssr-B-DNA-A36.pdb --frame=A.1:wc -o=expt-ref1.pdb

Now expt-ref1.pdb and the rebuilt structure dssr-B-DNA-A36-rb10.5.pdb would be in the same coordinate system. This is the simplest way to align the two structures. See the DSSR User Manual for more details.

It is also possible to transform the rebuild structure into the coordinate system of the original structure. It is a bit more complicated. I will consider write a blog post on this topic in the future.

You can easily verify that rebuild structure and the original structure are indeed very similar in two ways: One way is to re-analyze the rebuilt structure with DSSR, you will see that the base-pair parameters are very close to the ones for the original structure. The other way is perform a superimposition of the two structures, and  you will see that the RMSD for the base atoms is close to 0. See the commands below:

Code: [Select]

# extract base atoms from the original structure
x3dna-dssr -i=dssr-B-DNA-A36.pdb --select-base -o=exp-base.pdb

# extract base atoms from the rebuilt structure
x3dna-dssr -i=dssr-B-DNA-A36-rb10.5.pdb --select-base -o=rebuild-base.pdb

# the RMSD between exp-base.pdb and rebuild-base.pdb is 0.016.
For your verification, exp-base.pdb and rebuild-base.pdb are attached to this post.

While we're at it, here's an excerpt worth taking from the DSSR User Manual (5.3 Customized structures):

The 3DNA rebuild program complements analyze by reinforcing and verifying it. These two programs are a defining feature of 3DNA (Lu and Olson, 2003, 2008; Li et al., 2019). The 3DNA analyze and rebuild programs are based on SCHNAaP/SCHNArP (Lu et al., 1997a,b) which implement and extend the rigorous CEHS algorithm (El Hassan and Calladine, 1995) for the analysis/rebuilding of DNA duplexes.

The reversibility of the analysis/rebuilding programs in 3DNA allows scientists to ask what-if questions. By first deriving a complete set of base-pair parameters from an experimental structure, they can then systematically introduce changes in these parameters to see what happens to the shapes of the resulting 3D structures. This is a simple, yet powerful concept. 3DNA is the only widely used DNA/RNA structural bioinformatics tool with this feature. It has led to the discovery of a novel roll-and-slide mechanism to account for DNA folding in chromatin (Tolstorukov et al., 2007). Using modeling studies enabled by 3DNA, the Johnson lab at UCLA has revealed slide as a key parameter (along with roll and twist) in mediating DNA minor groove width (Hancock et al., 2019; Chen et al., 2018; Hancock et al., 2016, 2013; Stella et al., 2010).

The DSSR analyze module has completely surpassed the 3DNA analyze program (see Section 3.18). Similarly, the rebuild module in DSSR replaces the 3DNA rebuild program, with enriched functionality and improved usability. The module must be run as x3dna-dssr rebuild, just like a sub-command in Git.

25

RNA structures (DSSR) / Question about axis tilt after reconstruction of B-DNA using x3dna-dssr

« Last post by GengshiWu on July 31, 2025, 10:46:10 pm »

Hi Xiang-Jun, I have been working with the 3DNA DSSR tools to generate a B-DNA helix and encountered an unexpected issue with the axis alignment after reconstruction. Here are the steps that I performed:

1. Generated a 36 bp B-DNA helix using: x3dna-dssr fiber --model=B-DNA --seq=A36 -o=dssr-B-DNA-A36.pdb
    -When I open the dssr-B-DNA-A36.pdb file that I generated in UCSF Chimera, the helix axis aligns perfectly with the 3D coordinate z-axis.

2. Extracted parameters using: x3dna-dssr analyze --rebuild -i=dssr-B-DNA-A36.pdb -o=dssr-B-DNA-A36-expt.out
    -Then, I renamed the extracted step and helical parameter files for clarity: mv dssr-dsStepPars.txt dssr-B-DNA-A36-step.txt  mv dssr-dsHeliPars.txt dssr-B-DNA-A36-heli.txt

3. Reconstructed the structure using the step parameter file with: x3dna-dssr rebuild --backbone=B-DNA --par-file=dssr-B-DNA-A36-step.txt -o=dssr-B-DNA-A36-rb10.5.pdb
    - However, when I open the reconstructed pdb file in Chimera, the helix axis is slightly tilted relative to the z-axis.

Could you please advise whether this tilt is expected due to reconstruction? Or is there a recommended way to maintain the original axis alignment during rebuilding?

Thanks!

26

General discussions (Q&As) / Re: Download error for 3DNA v2.4.8-2023nov10 C Source Code

« Last post by nirtonik on July 27, 2025, 08:35:44 pm »

It is working, thank you so much!

27

General discussions (Q&As) / Re: Download error for 3DNA v2.4.8-2023nov10 C Source Code

« Last post by xiangjun on July 27, 2025, 04:48:46 pm »

Hi Arman Alborzi,

Thank you for reporting this issue, which has now been resolved. I am currently in the process of updating and reorganizing resources on our servers, which may cause temporary disruptions. Please try again and let me know if the problem persists.

Best regards,

Xiang-Jun

28

General discussions (Q&As) / Download error for 3DNA v2.4.8-2023nov10 C Source Code

« Last post by nirtonik on July 27, 2025, 03:34:26 pm »

Hello Dr. Xiang‑Jun Lu and 3DNA community,

I’m using DSSR v2.5.4 on PDB 1EHZ and need to reproduce DSSR’s base‑reference frames in my own Python code. To do this, I require the classic X3DNA v2.4 “atomic.base” template file (found in config/atomic.base of the full C‑source distribution) so I can align the standard guanine (2MG) template to my observed atom coordinates.

On the download page I see the entries:

  3DNA v2.4.8‑2023nov10; the classic X3DNA suite… 
  • Linux 64‑bit (including C source code) 
  • macOS M2 (including C source code) 
  • C source code 

-but every link appears broken (“cannot reach this page”) and I cannot download the archive.
Without config/atomic.base I cannot extract the G/2MG template coordinates needed
Could someone please:

1. Provide a working download link for the X3DNA v2.4 C‑source package,

Thank you very much for your help!

- Arman Alborzi 

29

General discussions (Q&As) / Re: Rebuild B-DNA

« Last post by xiangjun on July 25, 2025, 11:33:04 am »

The thymine base in DNA features a methyl group at the C5 position, previously designated as C5M. The updated convention now refers to this as C7. DSSR v2.6.0, available on the CTV download page, has renamed the thymine methyl group at the C5 position from C5M to C7. This revision ensures that DSSR's atomic model rebuilding aligns with the current nomenclature.

The make this response complete, here are the DSSR commands for generating the B-DNA model based on PDB entry 1hlo:

Code: Bash

1. # Verify DSSR version
2. x3dna-dssr -v
3.       # v2.6.0-2025jul24
4.  
5. # PDB file 1hlo.pdb is downloaded from RCSB PDB
6. x3dna-dssr analyze --input=1hlo.pdb --rebuild-parameters
7.  
8. # The above command generates file dssr-dsStepPars.txt
9. x3dna-dssr rebuild --backbone=B-DNA --par-file=dssr-dsStepPars.txt --o=new2.pdb

Attachments:

• dssr-dsStepPars.txt
• new2.pdb

30

Bug reports / Re: When analyzing multiple frames with --nmr, DSSR gets slower with each frame

« Last post by xiangjun on July 23, 2025, 11:29:24 pm »

I have updated DSSR Academic to version 2.6.0, which significantly speeds up the analysis of multiple frames of MD trajectories. The default settings will no longer experience slowdowns with later frames. The runtime should now scale linearly with the number of frames, as expected.

The new DSSR Academic v2.6.0 will shortly be available on the CTV download page, expected to be released within the next few days.

Note added on 2025-07-25: DSSR v2.6.0 is now available on CTV download page