Recent Posts

11

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

« Last post by xiangjun 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

12

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

« Last post by tengxj12345 on May 01, 2025, 12:28:19 pm »

Thanks for your detailed explanation. I will check it out.

13

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

« Last post by xiangjun 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

« Last post by tengxj12345 on April 30, 2025, 10:44:44 pm »

Sure. I attached my pdb file. I uploaded to the webserver and generated summary.txt.

The last section of the file (Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step) was then used to draw the centroids. I can get the same results bu running it on my local computer (find_pair and analyze).

15

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

« Last post by xiangjun 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

16

RNA structures (DSSR) / Contour of dsDNA/dsRNA

« Last post by tengxj12345 on April 30, 2025, 09:48:25 pm »

Hello,

I tried to get the contour of dsDNA/dsRNA structures. I think the output from helical section should be it. When I plot the positions of local helical axis along with my pdb, 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?

Thanks,
Xiaojing Teng

17

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

« Last post by xiangjun on April 30, 2025, 08:40:24 am »

Hi Di,

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

Best regards,

Xiang-Jun

18

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

« Last post by xiangjun 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

19

RNA structures (DSSR) / Building G-quadruplexes

« Last post by shr on April 29, 2025, 12:03:42 pm »

I am writing this code for GQ structure generation from sequence which can be found here https://github.com/sHr3y4s1/GQ-gen. I have just written this for the first G-track but this can be iterated to create more and then building in loops. I have attached an image of the output of this code. I don't know if this is the best way to do it but I am trying to create a basic canonical structure with specific topologies which can be energy minimized with an ion. I was thinking of a similar way for creating circular Z-DNA structures as well.

20

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

« Last post by xiangjun 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