Recent Posts

1

FAQs / Re: Where to download x3DNA

« Last post by xiangjun on Yesterday at 10:24:39 am »

Hi Changdong,

Thank you for the follow-up.

I would like to clarify that the licensing for DSSR is managed by Columbia Technology Ventures (CTVs). While DSSR has a large global community with hundreds of academic users, licenses are generally not issued to institutions in certain countries due to institutional compliance and administrative policies. Unfortunately, this means that even if an academic request is submitted, it may be restricted based on the location of the host institution.

However, you can still access DSSR through the following options:

• DSSR v1.9.10-2020apr23: This version is available for download directly from the 3DNA Forum. It corresponds to the paper "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL" (2020) published in Nucleic Acids Research.
• wDSSR: You can use the recently released web interface for DSSR at https://web.x3dna-dssr.org/.
  

I appreciate your interest in the software and your understanding of these constraints.

Best regards,

Xiang-Jun

2

FAQs / Re: Where to download x3DNA

« Last post by amtblcd on Yesterday at 12:48:41 am »

Hi Xiang-Jun,

Thanks for your reply. Understood — I’ll follow up there and avoid duplicate posts.

I also wanted to note that I’m still unable to download DSSR v2.8.1-2026mar12, even though I submitted an academic account request for a free seat.

Best regards,
Changdong

3

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

« Last post by shuxiang on April 25, 2026, 10:20:30 pm »

Hi Mihir,

The problem has been fixed. Please have a try and let us know if you have any questions.

Best,
Shuxiang

4

FAQs / Re: Where to download x3DNA

« Last post by xiangjun on April 24, 2026, 07:22:52 am »

Hi Changdong,

Thanks for your interest in 3DNA/DSSR. Your question has been addressed in another thread: License requested.

Please don’t hesitate to ask questions on the forum, but kindly avoid posting the same query in multiple threads to keep the discussion organized.

Best regards,

Xiang-Jun

5

RNA structures (DSSR) / Re: License requested

« Last post by xiangjun on April 24, 2026, 07:13:13 am »

Hi Changdong,

Thanks for reaching out. You should now be able to see the Download link at the very top of the forum.

Due to a high volume of spam, I have implemented a filter for registered users. Although your account was created in 2018, it remained in a "Pending" category because you had not yet posted on the 3DNA Forum. Once a user's first post is approved, the Download link becomes visible automatically.

Best regards,

Xiang-Jun

6

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

7

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

8

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

9

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

10

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