Recent Posts

11

FAQs / Re: Where to download x3DNA

« Last post by amtblcd on April 24, 2026, 12:26:11 am »

Hi,

I registered several years ago using my academic email address, but I am currently unable to access the download page.

Could you please assist me with this issue?

Many thanks.
Changdong

12

RNA structures (DSSR) / Re: License requested

« Last post by amtblcd on April 22, 2026, 03:38:09 am »

Hi,

I have the same problem. Even after following the instructions and completing the registration, it still shows as “Site announcement”. 

Could you please advise on what I should do next?

Thank you very much.

Best regards,
Changdong

13

Bug reports / Re: Missing DNA bases with negative residue number

« Last post by xiangjun on April 14, 2026, 02:12:50 pm »

Hi Mihir,

Great catch! I have successfully reproduced the issue. The bug is due to a parsing error within the wDSSR web interface. As shown below, the core DSSR engine itself handles negative residue numbering without any issues.

Execute the following command to see the enumeration:

Code: [Select]

x3dna-dssr mutate -i=9GBV.pdb --enum
An excerpt of the output is as follows:

# For each entry to be mutated, remove the leading #, and add to=base

# To mutate A.A9 to G in PDB entry 1ehz (tRNA):
#          #  chain=A name=A num=9  #9  A.A9
#       --->  chain=A name=A num=9 to=G

# To mutate B.DT19 to DC in PDB entry 355d (B-DNA):
#          #  chain=B name=DT num=19  #19  B.DT19, pairedNt=A.DA6
#       --->  chain=B name=DT num=19 to=DC

# Empty or comment (starting with #) lines are ignored.

#  chain=E name=DT num=-37  #1  E.DT-37, pairedNt=F.DA80
#  chain=E name=DG num=-36  #2  E.DG-36, pairedNt=F.DC79
#  chain=E name=DC num=-35  #3  E.DC-35, pairedNt=F.DG78
#  chain=E name=DC num=-34  #4  E.DC-34, pairedNt=F.DG77
#  chain=E name=DA num=-33  #5  E.DA-33, pairedNt=F.DT76
#  chain=E name=DT num=-32  #6  E.DT-32, pairedNt=F.DA75
#  chain=E name=DC num=-31  #7  E.DC-31, pairedNt=F.DG74
#  chain=E name=DA num=-30  #8  E.DA-30, pairedNt=F.DT73
#  chain=E name=DG num=-29  #9  E.DG-29, pairedNt=F.DC72
#  chain=E name=DA num=-28  #10  E.DA-28, pairedNt=F.DT71
#  chain=E name=DA num=-27  #11  E.DA-27, pairedNt=F.DT70
#  chain=E name=DA num=-26  #12  E.DA-26, pairedNt=F.DT69
#  chain=E name=DA num=-25  #13  E.DA-25, pairedNt=F.DT68
#  chain=E name=DC num=-24  #14  E.DC-24, pairedNt=F.DG67
......

We will resolve this wDSSR error shortly. In the meantime, please continue using the tool and report any further issues you encounter.

If it is an option for your workflow, I recommend installing the standalone version of DSSR on your computer and using the command-line interface directly.

Best regards,

Xiang-Jun

14

Bug reports / Re: Missing DNA bases with negative residue number

« Last post by mihir41@terpmail.umd.edu on April 14, 2026, 01:23:48 pm »

Hello Xiang-Jun,

I used the online tool for DNA mutation.

On the page https://web.x3dna-dssr.org/mutation

I entered PDB ID: "9GBV" in the left box. Then clicked on the "List all bases" button.

On the next page, I see bases listed for chains E (from resid number 0 to 121) and F (from resid number 0 to 80).

However, if you check the sequence map on the RCSB (https://www.rcsb.org/3d-view/9GBV), you would see that chain E residues range from -37 to 121, and chain F residues range from -78 to 80.

Please let me know if you need more information.

Best,
Mihir

15

Bug reports / Re: Missing DNA bases with negative residue number

« Last post by xiangjun on April 14, 2026, 11:34:06 am »

Hi,

Thank you for using our tools and for reaching out on the forum.

To help us investigate this further, could you please provide a step-by-step description of your workflow? Specifically, please include the exact commands or options you used so that we can reproduce the issue on our end. This will help us determine why the residues with negative numbers are not being displayed as expected.

Best regards,

Xiang-Jun

16

Bug reports / Missing DNA bases with negative residue number

« Last post by mihir41@terpmail.umd.edu on April 14, 2026, 08:51:15 am »

The PDB ID: 9GBV has 217 bp long dsDNA (Chain E & F). I plan to perform a mutation in some bases. But many of the bases are not displayed. Specifically, all the bases having a negative residue number are omitted by the portal.

17

General discussions (Q&As) / Re: Approach for building G-quadruplex models with 3'-3' and 5'-5'polarity inversion

« Last post by xiangjun on April 06, 2026, 02:02:29 pm »

Hi muha,

Thanks for posting on the Forum, and sorry for the late reply.

I understand your aim to build a unimolecular G-quadruplex model with alternating 5'-3', 3'-3', 3'-5', and 5'-5' linkages. DSSR does not have a built-in option for building such models, and I am not aware of any other software that can do this. In my understanding, this would require a combination of DSSR and a 3D manual editing tool to adjust the polarity of the linkages.

As far as analysis is concerned, DSSR should be able to identify G-tetrads, and may take each tract as broken chains. We need specific examples to show how DSSR should behave in these cases. I will consider modifying DSSR to handle these cases if feasible.

Best regards,

Xiang-Jun

18

FAQs / Re: Where to download x3DNA

« Last post by xiangjun on April 01, 2026, 03:03:00 pm »

Hi Luca,

Thanks for your interest in 3DNA. You should now be able to see the download page on the 3DNA Forum.

Best regards,

Xiang-Jun

19

Site announcements / Staff Associate II (Computational Structural Biology) at Columbia University

« Last post by xiangjun on April 01, 2026, 01:36:23 pm »

The X3DNA-DSSR resource is at the forefront of structural bioinformatics, developing advanced tools for analyzing and modeling nucleic acid structures. We are seeking a highly motivated Staff Associate II to join our team and contribute to our next-generation analysis and visualization engine.

To see our resource in action, please visit wDSSR, our new web interface for dissecting and modeling 3D nucleic acid structures: https://web.x3dna-dssr.org/.

We are looking for a candidate with a strong scientific background in structural biology or bioinformatics and a desire to contribute to peer-reviewed publications through community-driven data analysis. We value individuals who are eager to learn, adapt to new technical challenges, and support the global research community.

For the full job description and to submit your application, please visit the official Columbia University posting:
https://apply.interfolio.com/183705

20

FAQs / Re: Where to download x3DNA

« Last post by 胡俊杰 on March 31, 2026, 02:15:19 am »

Hello!

I have received the e-mail confirming the registration but still don't see the download section.
Could you please give me access to that.

Many Thanks

Luca