Messages

1

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

2

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

3

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.

4

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

5

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

6

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

7

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

8

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

9

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

10

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

11

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

12

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

13

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

14

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

15

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

16

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

17

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

18

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

« on: April 25, 2025, 07:40:54 am »

Hi Di,

This looks good. Please provide the commands used to generate the structures, for example, as I did in the blogpost on "Building extended Z-DNA structures with backbones using DSSR". Every detail counts for reproducibility.

Moreover, I would also consider the case where C-G pairs instead of G-C pairs are present in the structure. Or all 168 pairs with CGCG... sequence. I've thought about the case, and I think what we are trying to acheive fit under the general category of mutated backbones, given the atomic coordinates of base atoms. This is in contrast to the mutating bases feature currently implemented in `mutate_bases` in 3DNA and the `x3dna-dssr mutate` subcommand in DSSR.

Best regards,

Xiang-Jun

19

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

« on: April 24, 2025, 11:07:20 pm »

Hi @Di_Liu,

I tried to make some progress on constructing a 168-bp circular Z-DNA structure. What I have achieved so far is determining the positions of the repeating units (each being a CG dimer) along the ring. Each position currently serves as a placeholder (a G:C pair; 84 in total), to be replaced by a Z-DNA dimer unit.

I'm attaching a screenshot of the current structure, as well as the corresponding PDB file. I think Xiang-Jun might be able to work his "tasks" magic to align and insert the Z-DNA dimer units into the specified positions.

Nice progress! Using DSSR, I can see clearly the 84 isolated G-C pairs along the circular structure. I will consider adding an option to "x3dna-dssr tasks" subcommand to replace these G-C pairs with GpC dinucleotide steps. Before doing that, it helps to manually replace a few of these G-C pairs with GpC steps to see how the structure looks like. These examples would also server as test cases to validate the new option.

If you think this direction makes sense, I’d be happy to post the detailed process of how I constructed this circle.

Yes, it does make sense. Please go ahead and post the details of your construction process. It may take several iterations to get the desired results. The more concrete our discussions are, the better we can understand each other.

Best regards,

Xiang-Jun

20

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

« on: April 24, 2025, 10:50:29 pm »

Hi @shr,

My work focuses on molecular dynamics simulations of Z-DNA and its interactions with binding proteins. I'm particularly interested in understanding the mechanisms that stabilize Z-DNA, which is inherently less stable than B-DNA. To explore this, I used the crystal structure of the ADAR1 protein bound to a short Z-DNA segment. Since the original segment was quite short, I wanted to extend the Z-DNA backbone. With your help, I was able to successfully simulate this extended structure.

Thanks for the background information about your work on Z-DNA structure. I am glad to hear that the extended Z-DNA structure allowed you to perform your simulations.

However, I encountered challenges in reproducing the specific protein–Z-DNA interactions observed in the crystal structure during my simulations. I believe this is due to multiple non-specific interactions forming between the DNA and the protein, which may mask or override the specific contacts I'm trying to study. It is not a Z-DNA remodeling problem but I am working on understanding Z-DNA stability.

Thank you for sharing your story. Z-DNA modeling is just the first step in understanding its role in biological processes. The other part is beyond the scope of DSSR.

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.

As @Di_Liu suggested, I believe a similar model-building strategy could be applied to Z-DNA, to help generate consistent and realistic structures. What do you think about this approach or direction?

Yes, I believe the underlying principles can be generally applicable, including Z-DNA or right-handed A-/B-DNA. The approach in "Building extended Z-DNA structures with backbones using DSSR" is virtually the same as the one used for "create a 26 bp RNA from a 13 bp system".

Please provide more details. Working together with @Di_Liu, we should be able to come up with some interesting results.

Best regards,

Xiang-Jun


Best regards,

Xiang-Jun

21

General discussions (Q&As) / Re: Rebuilding Z-DNA

« on: April 24, 2025, 08:30:01 am »

I apologize once again.

I appreciate your attitude and the effort you put into bringing up this interesting topic on the Forum. This case also reminds me that I should be a bit more proactive in engaging with users like you. I always respond directly to users' questions, no matter how minor. Whenever necessary, I ask for clarification to ensure I understand and address their issues correctly. However, if there’s no response, I normally shy away from pushing users further—even though I may have done extra work to make sure I’m on the right track.

I look forward to the blogpost and will check out the thread "Rebuilding circular Z-DNA".

Done. Please see the blogpost Building extended Z-DNA structures with backbones using DSSR. Following the steps in the blogpost, users should be able to build extended Z-DNA structures exactly as described.

I would be happy to contribute in any way I can.

I noticed your follow-up post and the one from @Di_Liu on the new thread Rebuilding circular Z-DNA under the section 'RNA structures (DSSR).' This kind of participation is exactly what I have in mind for the forum. I will get back to you over there soon.

Working together, we should be able to come up with a solution that not only solves the problem at hand but also benefits the community. DSSR would become even more powerful!

Best regards,

Xiang-Jun

22

RNA structures (DSSR) / Re: Can x3dna-dssr correctly handle N1-methyl-pseudouridine?

« on: April 22, 2025, 06:17:34 pm »

Hi Di,

Thanks for the detailed response. I can only wish that all users are just like you in providing such helpful feedback. Over the years, it is users like you who have motivated me to keep working on DSSR ...

Best regards,

Xiang-Jun

23

General discussions (Q&As) / MOVED: Rebuilding circular Z-DNA

« on: April 22, 2025, 12:14:22 pm »

This topic has been moved to RNA structures (DSSR).

http://forum.x3dna.org/index.php?topic=1045.0

24

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

« on: April 22, 2025, 12:13:54 pm »

Hi Di,

Thanks for chiming in on the topic on modeling Z-DNA structures with proper backbones. User @shr "would also look forward to Z-DNA backbones being included in DSSR modeling functionalities."

Let's continue the discussion through this thread. Your special interest in circular Z-DNA structures will also be taken into account.

In addition to splitting the topic as a new thread, I have also moved the thread under the Section on RNA structures (DSSR) from "General discussions (Q&As)". I aim to develop this feature within DSSR. As noted previously, the classic 3DNA suite of programs has been superseded by DSSR.

If you and @shr could share what you have done so far, I would very much like to see. The more concrete examples, the better.

Best regards,

Xiang-Jun

25

RNA structures (DSSR) / Re: Can x3dna-dssr correctly handle N1-methyl-pseudouridine?

« on: April 22, 2025, 12:01:47 pm »

Hi Di,

As a follow-up to my previous response to your question, I have just written up a blog post on this topic: See Mapping of modified nucleotides in DSSR. In particular, from the listed ANSI C code, you should find the answer on how DSSR uses atomic connectivity to decide on pseudouridine modifications.

Best regards,

Xiang-Jun