Messages

1

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

« 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

2

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

« 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.

3

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

« 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

4

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

« 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

5

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

« 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

6

DNA/RNA-protein interactions (SNAP) / Re: Implement Json

« on: July 23, 2025, 11:12:13 pm »

As a follow up of the previous response, I would like to let the community know that as of DSSR Academic v2.6.0, the `--json` option is available for the SNAP subcommand. The new DSSR Academic v2.6.0 should be available in the CTV download page soon (in the next few days).

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

7

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

« on: July 06, 2025, 10:41:34 am »

Thanks for your feedback.

I've revised DSSR to replace C5M with C7 for thymine in A- and B-DNA. See the attached `new2.pdb` file.

As a side note, you could use the following command with the DSSR version you currently have installed:

Code: [Select]

x3dna-dssr mutate -i=new.pdb --entry='name=T to=T' -o=newx.pdb
Basically, it mutats T to T using the `mutate` subcommand. The net effect is C5M being replaced with C7 (see attached).

Best regards,

Xiang-Jun

8

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

« on: July 05, 2025, 11:14:02 pm »

Hi,

Thanks for using DSSR and for posting your question on the Forum. The two DSSR commands you used help illuminate the question well, and the snippets from your `new.pdb` file clearly show the issue.

However, I noticed that in the rebuilt DNA structure (new.pdb), all thymine bases appear to be methylated—specifically, the C5M atom shows up in the output. There is no methylation in my initial input file(1hlo.pdb)

The thymine base in DNA has a methyl group at the C5 position, which is named differently across various versions of the PDB
format. Historically, it was referred to as C5M, but in more recent versions (e.g., in `1hlo`), it is labeled as C7. For further
details, please refer to my blog post titled "Different names for the methyl group in DNA and RNA structures" at
https://x3dna.org/articles/different-names-for-the-methyl-group-in-dna-and-rna-structures

The presence of `C5M` in your `new.pdb` is because the building block in DSSR currently uses `C5M` to denote the methyl group on thymine instead of `C7`. Since you raised this point, I am considering updating DSSR to use `C7` for thymine in future versions. In the meantime, you can simply replace `C5M` with `C7` in your `new.pdb` file.

Best regads,

Xiang-Jun

9

RNA structures (DSSR) / Re: Building G-quadruplexes

« on: June 20, 2025, 10:56:12 am »

Hi,

Thanks for posting back and following up on the question about modeling G-quadruplexes. As mentioned in my May 05 post, G4 modeling are "experimental (and undocumented) features" in DSSR, and need to be further developed. DSSR is not open-source, and the Columbia Technologies Ventures (CTV) is in charge of licensing the command-line version of DSSR.

Best regards,

Xiang-Jun

10

DNA/RNA-protein interactions (SNAP) / Re: Implement Json

« on: June 13, 2025, 04:19:01 pm »

Hi,

Thanks for using SNAP/DSSR and for posting your question on the Forum.

The --json option is available in the DSSR Pro version (x3dna-dssr snap --json) . This is one of the few features that is currently not enabled in the free DSSR Basic Academic version. No paper on SNAP has been published yet. Some features need further developments and better documentation. I may consider enable more Pro features in the Basic version in the future.

The general principle of 3DNA/DSSR is to ensure that published results and documented features (in the DSSR Manual) are reproducible. DSSR has more to offer than those published/documented.

Best regards,

Xiang-Jun

11

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

« on: June 13, 2025, 10:36:42 am »

It sounds like a good suggestion. I will think about it.

12

RNA structures (DSSR) / Re: Using --helical-axis with the --nmr option in DSSR

« on: June 12, 2025, 02:57:39 pm »

Hi,

Thanks for your kind words about DSSR. Please try the --more option which will output "helical-axis", "point-one" and "point-one" as documented in the DSSR User Manual. You could parse the corresponding output for each model and start from there to calculate the bending angle.

Hope this helps.

Xiang-Jun

13

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

« on: June 12, 2025, 02:51:55 pm »

Hi,

Thanks for using DSSR and for posting your question on the Forum. I am aware of the issue you are describing. The initial design of the --nmr option allows for flexibility of user-selected frames/models (e.g., --nmr=3+5+6:9 as described in the User Manual). For each frame/model, DSSR re-reads the input file from the beginning, which causes the slowdown as you observed. There is no memory leak, as you can verify with valgrind or similar tools.

DSSR Pro version allows for sequential processing of all the frames in a single pass, which leads to faster performance (scale linearly with the number of frames).

Best regards,

Xiang-Jun

14

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« on: June 03, 2025, 12:42:43 am »

Hi Di,

Thanks for sharing the detailed steps you used to build the Z-DNA circle. What you called Y-shift and Z-shift are Slide and Rise, respectively, in the literature. Slide is an important parameter in determining DNA shapes, see "A Novel Roll-and-Slide Mechanism of DNA Folding in Chromatin: Implications for Nucleosome Positioning" and "The shape of the DNA minor groove directs binding by the DNA-bending protein Fis". It is also crucial for producing circular DNA structures, as you noticed.

Given below is the DSSR commands I used to generate the ZDNA-circle.pdb file I posted previously, plus further steps to improve the visualization of the 3D structure.

Code: Bash

1. # The starting point is your twist60-G84-scaled.pdb. Here only G on chain A is selected.
2. x3dna-dssr -i=twist60-G84-scaled.pdb --select-chain=A -o=chainA.pdb
3.  
4. # Extract a GpC step in Z-DNA conformation, and re-orient it in the reference frame of the first G (on Chain A)
5. x3dna-dssr fiber --z-dna --repeat=1 -o=fiber-GpC.pdb
6. x3dna-dssr -i=fiber-GpC.pdb --frame=A.1 -o=frame___Z.pdb
7.  
8. # Now mutate each G to a Z-DNA GpC step (frame___Z.pdb). The --mutate-type option is new in DSSR v2.5.3
9. #      "whole" to include backbone, and "raw-id" to keep the original identification of the atoms
10. x3dna-dssr mutate -i=chainA.pdb --entry="name=G to=Z" -o=ZDNA-circle.pdb --mutate-type=whole-raw-id
11.  
12. # The following steps would lead to better visualization of 3D structures
13. x3dna-dssr --order-residue -i=ZDNA-circle.pdb -o=temp_order.pdb --po-bond=3.6
14. x3dna-dssr --renumber-residue -i=temp_order.pdb -o=temp_renum.pdb
15. x3dna-dssr --connect-file -i=temp_renum.pdb -o=ZDNA-circle2.pdb --po-bond=3.6

The ZDNA-circle2.pdb and PyMOL-rendered image are attached. For completeness of this post, I have also attached twist60-G84-scaled.pdb from your previous post. With DSSR v2.5.3, users should be able to follow the above steps, and reproduce the results without any issues.

The overall strategy should be clear: in essence, the commands simply replace the 84 Gs with GpC dinucleotides steps in Z-DNA conformation. The method is generally applicable to other DNA/RNA modeling tasks, as demonstrated in my blogpost mentioned earlier "Mutate backbone of DNA and RNA structures". The integrative nature of DSSR is a key strength, and the automation it enables stands out when compared with alternative tools.

There are still areas that require refinement. I am more than willing to enhance the modeling capabilities in future releases of DSSR based on your feedback.

Best regards,

Xiang-Jun

15

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« on: June 02, 2025, 12:50:18 am »

Hi Di,

Thanks for your confirmation. See my blog post Mutate backbone of DNA and RNA structures. The x3dna-dssr mutate sub command can now mutate a base to another fragment with backbone and/or more than one nucleotides. This make it a generally applicable modeling tool within DSSR.

I will post details on how the circular Z-DNA was generated in the next couple of days. We can polish the procedure together to better fit your needs, and hopefully it would be useful to other users as well.

Best regards,

Xiang-Jun

16

RNA structures (DSSR) / Re: License requested

« on: May 31, 2025, 11:40:43 am »

Hi,

Thanks for your interest in DSSR, and for posting on this forum. I am aware of the issue, and put the following note in the Download instructions.

DSSR v1.9.10-2020apr23 --- This version corresponds to the paper "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL" (2020) in Nucleic Acids Research. From version 2.0 (released around the summer of 2020), DSSR has been licensed by the Columbia Technology Ventures (CTV), who manages the free DSSR Academic licenses as well as paid DSSR Pro licenses for both academic and commercial users. I've lately learned of academic users from certain countries having trouble in getting DSSR Academic licenses. This pre-licensed version is provided (as is) here to fill the gap: it is slightly outdated but still works well. Whenever possible, however, users should obtain the latest version of DSSR through CTV --- it is free for academic uses and fully supported by the NIH R24GM153869 grant.

Best regards,

Xiang-Jun

17

MD simulations / Re: Base pair number not staying constant in simulations

« on: May 21, 2025, 10:03:01 am »

Thanks for the detailed report. While @rkumar should be the primary contact for dnaMD related issues, I'd like to address the general question of why the base pair number not staying constant in simulations.

In 3DNA, the find_pair program is used to identify base pairs in an input structure. For MD trajectories, when each frame is processed with auto-detected base pairs, the numbers can fluctuate due to the dynamic nature of the system. The 3DNA suite includes the Ruby script x3dna_ensemble, and the beginning portion of the "x3dna_ensemble analyze -h" command is as follows. Basically, it requires a template base-pair input file, possibly generated with ‘find_pair’ and manually edited as necessary.

------------------------------------------------------------------------
Analyze a MODEL/ENDMDL delineated ensemble of NMR structures or MD
trajectories. All models must correspond to different conformations
of the same molecule. For the analysis of duplexes (default), a template
base-pair input file, generated with 'find_pair' and manually edited
as necessary, must be provided.

Usage:
        x3dna_ensemble analyze options
Examples:
        x3dna_ensemble analyze -b bpfile.dat -e sample_md0.pdb

In DSSR, the --nmr (or --md) option can be used with --pair-list-input to analyze MD trajectories with a customized set of base pairs of interest. See the DSSR User Manual for more details in Sections "3.13 The --nmr option" and "3.9 The --pair-list options".

Best regards,

Xiang-Jun

18

MD simulations / Re: Do I need gromacs to use dnaMD for simulations?

« on: May 16, 2025, 10:00:09 am »

Thanks for the x3DNA-DSSR software which works wonderfully for single PDBs.

Thanks for using DSSR and for posting your questions on the 3DNA Forum. As for the analysis of an ensemble, please see the DSSR manual , especially Section: "3.13 The --nmr option":

The DSSR --nmr (or --md) option automates the analysis of an ensemble, such as NMR structures in the PDB or snapshots from MD simulations. The input coordinates file must be in either the classic PDB format where each model is delineated by MODEL/ENDMDL tags, or the mmCIF format where each ATOM/HETATM record has an associated model number.
...
The --json option makes it easy to parse the output of multiple models pragmatically. In addition to NMR structures, trajectories from MD simulations can also be processed. Popular MD packages (AMBER, GROMACS, CHARMM, etc.) all have their own specialized binary formats for trajectories. By design, DSSR does not work on these binary files. They must be converted to the standard PDB or mmCIF format to be analyzed by DSSR. The combination of --nmr and --json makes DSSR directly accessible to the MD community.

I have some MD simulations I would like to analyze with dnaMD. I ran them with Amber but converted them to GROMACS .xtc + .pdb files for analysis.

Do I need GROMACS version of dnaMD to analyze simulations or can I use the Python module of dnaMD without GROMACS for simulations?

I am not a practitioner of MD simulations. Questions related to dnaMD are best answered by its developer: hopefully @rkumar will chime in. See the thread Update of do_x3dna package, which can be used with files generated by GROMACS.

PS. I am also lacking the link to download the 3DNA from the forum for some reason, my forum view is similar to unregistered users.

There have been too many spam registrations nowadays, so I must stay continuously vigilant to keep the Forum clean. You should now see the download link. Sorry for the inconvenience.

Best regards,

Xiang-Jun

19

RNA structures (DSSR) / Re: Building G-quadruplexes

« on: May 05, 2025, 10:57:00 am »

Hi shr,

Following the discussion in the previous thread on "Rebuilding circular Z-DNA", as quoted below:

In addition to Z-DNA, I also work on other non-canonical DNA structures, particularly G-quadruplexes (G4s). I’m developing a method to construct ideal G-quadruplex models from sequence data by first arranging guanine bases into tetrads, then building in the backbone and loop regions.

I am glad to hear about your work on G-quadruplexes. Actually, I have recently revised the G4 module in DSSR, fixed existing bugs, and added new features. The g4.x3dna.org website has undergone a complete overhaul, enabling users to upload their own structures for dynamic G4 analysis. Additionally, the DSSR-G4DB database is being actively updated on a weekly basis as new PDB entries are added. See the four blog posts comparing DSSR with other related analysis tools on G-quadruplexes: ASC-G4, Webba da Silva nomenclature, ElTetrado and related tools, and CIIS-GQ.

Moveover, I am also interested in modeling G-quadruplexes, taking G-tetrad as the building block. There are quite a few other threads in DSSR I'd like to pursue further in the future. I'd certainly like to hear more about your approach on modeling G-quadruplex.

I dug into the code of DSSR for modeling G-quadruplexes, and found the following experimental (and undocumented) features. DSSR can model G-quadruplexes using G-tetrad as the building block, and allows users to specify the number of G-tetrads and twist angle (among other things). See below for two examples: one with 3 layers of G-tetrads and 0 degrees of twist angle, and other with 6 layers and twist=36, respectively.

Best regards,

Xiang-Jun

20

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« on: May 05, 2025, 10:21:04 am »

Hi Di,

Are you still interested in the topic of modeling circular Z-DNA? I'm planning for a new release of DSSR (v2.5.3) which includes new features for modeling nucleic acid structures. It would be great to hear your feedback on how it works in your specific case.

I take user questions seriously as they provide valuable opportunities to enhance the software. Each piece of user feedback helps me think in ways I might not have considered otherwise. By analyzing feedback and integrating suggestions, DSSR becomes more robust and user-friendly. At the same time, I consistently adopt a systematic approach when introducing new features, ensuring they are thoroughly tested and reliable while addressing users' concerns.

Best regards,

Xiang-Jun

21

RNA structures (DSSR) / Re: Contour of dsDNA/dsRNA

« on: April 30, 2025, 11:38:47 pm »

Thanks for your clarification. The two attachments are very helpful. Now I can use the following 3DNA commands to reproduce the results:

Code: Bash

1. find_pair coor_7972.pdb | analyze

The output file "coor_7972.out" has exactly the same parameter as the attached file "summary.txt".

Now back to your question:

it seems quite strange. The helix doesn't follow the structure of my DNA well. Is there anything wrong, or there are other output can better represent the contour?

The "strange" behavior you are observing is due to the sensitivity of helical parameters to local structural variations. There is nothing wrong as far as 3DNA goes. To verify this, you could try the following two things:

* Build a perfectly regular fiber RNA duplex model using the command below, and repeat your procedure. You should see a straight helix as expected. For example, see Figures 1 and 9 of the 2003 3DNA paper.

Code: Bash

1. fiber -seq=AAAAAAAAAA -rna fiber-RNA-A10.pdb
2. # or better yet, using DSSR v2.5.2
3. x3dna-dssr fiber --rna-duplex --seq=A10 -o=dssr-fiber-RNA-A10.pdb

* With the parameters from 3DNA analyze output (bp_step.par or bp_helical.par), you can run rebuild to generate a structure. The RMSD between the original structure and the rebuilt one should be close to 0 for base + C1' atoms. If you analyze the rebuilt structure, you should get virtually identical helical parameters as for the original structure. The analyze/rebuild reversibility is one of the core features of 3DNA and DSSR, originating from the SCHNAaP/SCHNArP pair of programs based the CEHS algorithm.

Hope this helps! Basically, what you are observing is the expected behavior of 3DNA.

That being said, for visualization purposes, one might want to smooth the local variations using Bezier curves or similar methods.

Best regards,

Xiang-Jun

22

RNA structures (DSSR) / Re: Contour of dsDNA/dsRNA

« on: April 30, 2025, 10:31:11 pm »

Hi Xiaojing,

Thanks for posting on the 3DNA Forum. Could you please provide details about how you generated the contour plot for dsDNA/dsRNA you attached? These would include the PDB or mmCIF coordinates file, and the exact DSSR/3DNA commands you used. The goal is reproducibility and to help others understand the process better.

Best regards,

Xiang-Jun

23

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« on: April 30, 2025, 08:40:24 am »

Hi Di,

How about the attached results? Does it meet your expectations?

Best regards,

Xiang-Jun

24

RNA structures (DSSR) / Re: Building G-quadruplexes

« on: April 29, 2025, 02:01:05 pm »

Hi shr,

I've split your response from the thread "Rebuilding circular Z-DNA" into its own thread for better organization and discussion.

It a nice start with the first G-tetrad. Please add more features to your GQ-gen.py script so it can at least build a complete G-quadruplex structure. I'll chime in with some suggestions to your project, while I'm working on adding proper Z-DNA backbone to DSSR-enabled models.

Best regards,

Xiang-Jun

25

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« on: April 25, 2025, 02:34:26 pm »

Hi Di,

Thanks for providing further details on how the structure was generated. Such contextual information is always helpful and serves as a valuable reference for the automated approach we aim to develop.

I will take a closer look at the topic and hopefully could come up something to share by next week. Ad hoc solution is easier to implement but I am keen for a systematic approach as mentioned briefly in my previous response.

Best regards,

Xiang-Jun