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31

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

32

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

33

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

« Last post by xiangjun 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

34

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

« Last post by xiangjun 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

35

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

« Last post by Xuan Liu on July 06, 2025, 03:14:38 am »

Thank you very much for your reply!

36

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

« Last post by xiangjun 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

37

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

« Last post by Xuan Liu on July 05, 2025, 09:56:38 am »

Hi,

I am using DSSR v2.5.2 to build a DNA structure with the following command:
x3dna-dssr rebuild --backbone=B-DNA --par-file=dssr-dsStepPars.txt --o=new.pdb

The file dssr-dsStepPars.txt was generated using this command:
x3dna-dssr analyze --input=1hlo.pdb --rebuild-parameters

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)
Snippets of the new.pdb file showing the issue have been attached to this message.

Could you please help me understand why the C5M atom appears in the rebuilt structure? Also, how can I generate the DNA structure without this methylation (without C5M)?

Thank you!

38

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

« Last post by shr on June 23, 2025, 11:35:09 am »

Thank you for the response! I will keep working on the code on my end and figure out a way to make it work.

With regards
Shreyasi Das

39

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

« Last post by xiangjun 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

40

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

« Last post by shr on June 20, 2025, 02:38:28 am »

It looks like this can definitely be used as a building block. Is the DSSR code for G-Quadruplex open-source? If I may ask, would it be possible to look into the code? In my code, I tried to add more stacks but it seems a little tricky to do considering the backbone also needs to be bonded together.

With regards
Shreyasi Das