Recent Posts

21

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!

22

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

23

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!

24

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

25

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

26

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

27

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

« Last post by xiangjun 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

28

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

« Last post by kyle_ on June 13, 2025, 04:02:02 pm »

Hello,
I am using SNAP via `x3dna-dssr snap -i=my_file.pdb` and have found the output very useful, but am hoping to export it as JSON to automate some of my analysis. I see how I can run `x3dna-dssr -i=my_file.pdb --json`, and it seems that when `x3dna-snap` was packaged separately it had also a `--json` flag for this purpose (eg. https://x3dna.org/articles/h-bonds-reported-by-dssr-and-snap). Such a flag no longer seems to work with `x3dna-dssr snap -i=my_file.pdb --json`, so I am asking: does this JSON format functionality still exist for SNAP output? Perhaps it exists and this flag is not the way to access it.

29

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

« Last post by xiangjun on June 13, 2025, 10:36:42 am »

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

30

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

« Last post by rkpoppleton on June 13, 2025, 09:58:08 am »

I see.  That makes sense where the slowdown is coming from.  For what its worth, in tools I've worked on in the past, when we need to do random-access trajectory reading, we first read through the whole trajectory once and make an index of the byte offsets for the start of each frame.  That way you can jump to any arbitrary frame without having to search through the file each time.