Recent Posts

11

General discussions (Q&As) / Re: Download error for 3DNA v2.4.8-2023nov10 C Source Code

« Last post by xiangjun on July 27, 2025, 04:48:46 pm »

Hi Arman Alborzi,

Thank you for reporting this issue, which has now been resolved. I am currently in the process of updating and reorganizing resources on our servers, which may cause temporary disruptions. Please try again and let me know if the problem persists.

Best regards,

Xiang-Jun

12

General discussions (Q&As) / Download error for 3DNA v2.4.8-2023nov10 C Source Code

« Last post by nirtonik on July 27, 2025, 03:34:26 pm »

Hello Dr. Xiang‑Jun Lu and 3DNA community,

I’m using DSSR v2.5.4 on PDB 1EHZ and need to reproduce DSSR’s base‑reference frames in my own Python code. To do this, I require the classic X3DNA v2.4 “atomic.base” template file (found in config/atomic.base of the full C‑source distribution) so I can align the standard guanine (2MG) template to my observed atom coordinates.

On the download page I see the entries:

  3DNA v2.4.8‑2023nov10; the classic X3DNA suite… 
  • Linux 64‑bit (including C source code) 
  • macOS M2 (including C source code) 
  • C source code 

-but every link appears broken (“cannot reach this page”) and I cannot download the archive.
Without config/atomic.base I cannot extract the G/2MG template coordinates needed
Could someone please:

1. Provide a working download link for the X3DNA v2.4 C‑source package,

Thank you very much for your help!

- Arman Alborzi 

13

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

14

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

15

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

16

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

17

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!

18

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

19

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!

20

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