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31

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

« Last post by rkpoppleton on June 12, 2025, 08:27:14 am »

Hi!  Thanks for the excellent tool, DSSR has solved so many problems in my analysis of RNA MD simulations!  I am currently trying to calculate the angle between two helices in an RNA structure.  For any single configuration, I can use the --helical-axis option to get the helical axes as a .pdb file, which works very well.  However this file seems to be overwritten for every frame if you run DSSR on multiple frames with the --nmr option.  I looked around in the --json output, but I can't seem to find a per-model output there. 

Are the helix axes output anywhere and I just missed them, or is there something else I need to do to get the dssr-helicalAxes.pdb file on a per-model basis?

32

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

« Last post by xiangjun 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

33

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

« Last post by Di_Liu on June 02, 2025, 04:44:26 am »

Hi Xiang-Jun,

I've included my detailed procedure in this Evernote for your review: https://share.evernote.com/note/b6bd8283-bcad-58aa-0725-95dc61a9c6e0

I hope you can help explain why Y-shift is introduced when generating your B-DNA ring. Also, I think you would have a better idea than me of creating a Z-DNA ring with higher accuracy by taking into account the spatial relationship of the helical axis and the bp.

Thanks,

Di

34

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

« Last post by xiangjun 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

35

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

« Last post by Di_Liu on June 01, 2025, 09:08:25 pm »

Hi Xiang-Jun,

I checked your model, and I can confirm that it is what I wanted.

I'm also attaching the model I've built. The screenshot is a comparison of yours (blue) and mine (pink). I think we were using the G84 ring I've created, so our models can be overlayed. An extra step required for your model is to link the dinucleotide steps.

By the way, I think I figured out why I didn't get the email notification. I indeed received a notification on April 30, but I thought (mistakenly, probably due to the early morning...) I had already viewed the reply because you posted a reply on April 29, which was assumed to be the same message, so I didn't open a link for your April 30 message. I saw in the email that "More replies may be posted, but you won't receive any more notifications until you read the topic." I believe this setting is the reason I didn't the email notification of your follow-up message on May 5.

Best,

Di

36

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

« Last post by Di_Liu on June 01, 2025, 08:39:40 pm »

Hi Xiang-Jun,

Thanks a lot for your following-up of my questions!

I'm sorry that I didn't look back into this question. And I don't know why I didn't receive an email notification about your reply. I remember that I always received an email notification whenever there was a reply to my message in the past...

I logged in today because I also have made progress to create the Z-DNA ring during the weekend, and wanted to let you know. Do you want me to post the details of my procedure?

Thanks again for your work, and I will check your model and let you know my opinion!

Best,

Di

37

RNA structures (DSSR) / Re: License requested

« Last post by xiangjun 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

38

RNA structures (DSSR) / License requested

« Last post by moloch on May 31, 2025, 08:56:06 am »

I have requested the License, may I ask when it will be approved?

39

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

« Last post by rkumar on May 30, 2025, 01:09:55 pm »

Hi,

Apologies for the late reply. Please use  -ref option to keep the base-pairs constant. However, any parameters calculated for broken base-pairs will be of extreme values. If base-pairs are broken at the terminals, then those could be ignored during analysis by dnaMD.

Thanks,
Rajendra

40

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

« Last post by xiangjun 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