Recent Posts

51

RNA structures (DSSR) / Re: Can x3dna-dssr correctly handle N1-methyl-pseudouridine?

« Last post by xiangjun on April 22, 2025, 12:01:47 pm »

Hi Di,

As a follow-up to my previous response to your question, I have just written up a blog post on this topic: See Mapping of modified nucleotides in DSSR. In particular, from the listed ANSI C code, you should find the answer on how DSSR uses atomic connectivity to decide on pseudouridine modifications.

Best regards,

Xiang-Jun

52

General discussions (Q&As) / Re: Rebuilding Z-DNA

« Last post by xiangjun on April 22, 2025, 09:57:23 am »

Apologies for it took a while to reply. Thank you for your help with the structure! I used phenix to minimise like you suggested and I can use it for my analysis now.

Thanks for the confirmation that the DSSR modeled Z-DNA structure works for your case. It is through interactions with real-world users like you that makes DSSR relevant and useful.

Even though virtual, a forum thread is just like a conversation. I strive to respond to users' questions timely and concretely. Users who initiate a thread are expected to follow up with their progress and share their findings, or the lack thereof. It’s a two-way street, and I appreciate your engagement and contributions to the forum.

As a follow up, I am planing to write a blogpost to summarize the discussion and provide step-by-step details on how the extended Z-DNA structure was built using DSSR. This may take a couple of days, and I will provide a link here once it is ready.

I would also look forward to Z-DNA backbones being included in DSSR modeling functionalities.

I have split a new thread titled "Rebuilding circular Z-DNA". Please share your thoughts and suggestions on this topic over there.

Best regards.

Xiang-Jun

53

RNA structures (DSSR) / Re: Can x3dna-dssr correctly handle N1-methyl-pseudouridine?

« Last post by xiangjun on April 22, 2025, 09:08:26 am »

Hi Di,

Thanks for your well formulated question regarding x3dna-dssr’s support of N1-methyl-pseudouridine, B8H.

I understand that x3dna-dssr can handle pseudouridine (PDB Chem ID: PSU) correctly. I'm inquiring about its support for N1-methyl-pseudouridine (PDB Chem ID: B8H). Specifically,​ does x3dna-dssr recognize B8H based on its PDB chemical ID, or does it rely on atomic connectivity?

FYI, I've tested x3dna-dssr with PDB entries 8PFK and 8PFQ, both containing B8H, and the analysis proceeded without errors, with the results looking reasonable. However, given the unique C5-C1′ glycosidic bond for B8H, I want to confirm that x3dna-dssr interprets this modification accurately.

DSSR uses atomic connectivity to identify pseudouridine or its modified forms, including B8H. DSSR User Manual contains the following relevant information:

Note that pseudouridine, the most prevalently modified nt in RNA, is denoted P† in DSSR and the small case p is reserved for potential modified pseudouridines. ... footnote: †Not to be confused with the phosphorus atom in the backbone phosphate group. The distinction should be clear in context.

While anticipated, your reported case of B8H is the first time I see a modified pseudouridine. In DSSR output for 8PFK, you will see the following:

Code: Text

1. #x3dna-dssr -i=8PFK.pdb -o=8PFK.out
2.  
3. From 8PFK.out
4. ****************************************************************************
5. List of 1 type of 1 modified nucleotide
6.       nt    count  list
7.    1 B8H-p    1    A.B8H7
8.  
9. From dssr-torsions.txt
10. 7     p A.B8H7 ... chi -155.3(anti)

The chi for B8H is defined using O4'--C1'--C5--C4 instead of O4'--C1'--N1--C2, which would make no sense for pseudouridine. This is a little detail that DSSR pays attention to where other tools may not. See my blogpost Torsion angles from DSSR. You could easily verify this, using PyMOL for example, to measure the torsion angle by clicking four atoms in order.

The DSSR results for 8PFQ are also as expected with correct identification of B8H as a modified pseudouridine.

Further, is there a comprehensive list of modified nucleotides currently supported by x3dna-dssr?​ I came across these two pages (https://x3dna.org/highlights/automatic-identification-of-nucleotides ; https://x3dna.org/highlights/modified-nucleotides-in-the-pdb ), but could not find the exact answer.

To answer your question, here is an excerpt from my recent response to a similar inquiry:

Over the years, I've refined the heuristics of the mapping process. In the early days with 3DNA, I kept an ever increasing list of 'baselist.dat' with hundreds of entries like: MIA   a that maps MIA as a modified A, denoted as lowercase 'a'. In the current DSSR, I keep only the standard ones, with 48 entries total (see attached DSSR-baselist.txt). If a residue is not a standard one, the following function is called to do the mapping (DSSR performs filtering to decide if it is a nucleotide, and if so R or Y). DSSR also has a command-line option --nt-mapping as documented in the screenshot.

The DSSR-baselist.txt is attached for your reference. I am planning to write blogpost with details on this topic.

Best regards,

Xiang-Jun

54

RNA structures (DSSR) / Can x3dna-dssr correctly handle N1-methyl-pseudouridine?

« Last post by Di_Liu on April 22, 2025, 12:48:13 am »

Hi Xiang-Jun,

I understand that x3dna-dssr can handle pseudouridine (PDB Chem ID: PSU) correctly. I'm inquiring about its support for N1-methyl-pseudouridine (PDB Chem ID: B8H). Specifically,​ does x3dna-dssr recognize B8H based on its PDB chemical ID, or does it rely on atomic connectivity?

FYI, I've tested x3dna-dssr with PDB entries 8PFK and 8PFQ, both containing B8H, and the analysis proceeded without errors, with the results looking reasonable. However, given the unique C5-C1′ glycosidic bond for B8H, I want to confirm that x3dna-dssr interprets this modification accurately.

Further, is there a comprehensive list of modified nucleotides currently supported by x3dna-dssr?​ I came across these two pages (https://x3dna.org/highlights/automatic-identification-of-nucleotides ; https://x3dna.org/highlights/modified-nucleotides-in-the-pdb ), but could not find the exact answer.

Thank you for your assistance!

55

General discussions (Q&As) / Re: Rebuilding Z-DNA

« Last post by shr on April 21, 2025, 11:22:48 pm »

Apologies for it took a while to reply. Thank you for your help with the structure! I used phenix to minimise like you suggested and I can use it for my analysis now. I would also look forward to Z-DNA backbones being included in DSSR modeling functionalities.

56

RNA structures (DSSR) / Rebuilding circular Z-DNA

« Last post by Di_Liu on April 21, 2025, 08:10:12 pm »

Hi Xiang-Jun, I think three steps are needed for creating such a Z-DNA ring or more generally, any Z-form helical structures:

(1) Obtaining a helical parameter file in a similar way as the A- or B-form helices;
(2) Creating the atoms of the bases based on the helical parameter file;
(3) Putting the other atoms of the sugar and phosphate groups based on the position of the bases' atoms (there are only two conformations corresponding to the pyrimidines and purines, respectively).

Do you prefer that I start a new thread on this topic?

Thanks!

57

General discussions (Q&As) / Re: Rebuilding Z-DNA

« Last post by xiangjun on April 21, 2025, 04:20:23 pm »

Hi,

Thanks for chiming in on the discussion. Currently, DSSR can build DNA circles with right-handed helices, but not Z-DNA forms. The backbone of Z-DNA is dramatically different from that of B-DNA or A-DNA, and needs to be modeled differently. I'll look into how we can incorporate Z-DNA backbones into DSSR modeling functionalities, given enough interest from the community, and with a proper collaborator to work on it. See the DSSR-Jmol and DSSR-PyMOL integration for two concrete examples of what I have in mind for such collaborations.

As for the current thread, I'm hoping @shr could respond to my question on March 15, 2025:

Does the attached PDB file (with base schematic image) fulfill your needs?

See my recent post On registration and posting which includes a copy of "Registration Agreement for the Forum" at the bottom.

Best regards,

Xiang-Jun

58

General discussions (Q&As) / Re: Rebuilding Z-DNA

« Last post by Di_Liu on April 21, 2025, 04:48:00 am »

Hi Xiang-Jun, following up on the Z-DNA rebuilding, is there a way to create a Z-DNA circle? I think the difficulty lies in how to rebuild to create a backbone of Z-DNA using the helical parameters. Thanks!

59

Site announcements / On registration and posting

« Last post by xiangjun on April 19, 2025, 11:20:25 pm »

It has been 14 years since the Forum was created in 2011. Despite a four-year gap in NIH funding, we managed to keep the Forum operational. Maintaining and nurturing our community wasn't easy, but the users' enthusiasm in using and citing 3DNA/DSSR has kept us going. With the dedicated R24GM153869 grant, I am now committed to making the Forum even better.

Keeping the Forum spam-free is our top priority. In recent months, we have seen a dramatic increase in spams, which account for the majority of new registrations. That is why we have implemented 'Admin Approval' as the method of registration for new members. I carefully review each new registration to ensure only legitimate users are approved to join the Forum. Once approved, new users need to activate their accounts by clicking the activation link sent to their registered email address. I have noticed that some users did not activate their accounts upon approval. I normally send reminders to those inactivated users, but if they still do not respond in a few days, their registrations will be removed from the Forum.

It could also be the other way around: for example, the activation email sent from the 3DNA Forum might have been filtered out as spam by the user’s email agent. I have recently helped a few users with their registrations. If you have any questions or concerns about your registration, feel free to reach out to me directly via email. In today's age of AI, a personal touch goes a long way. Getting assistance directly from the developer ensures issues are resolved quickly and effectively.

I am dedicated to continuously enhancing X3DNA-DSSR, aiming to build it as a reputable brand symbolizing quality and value. Due to its exceptional functionality, ease of use, and direct support from the developer, X3DNA-DSSR significantly reduces the time and effort required compared to alternative solutions. Your comments, suggestions, and bug reports are greatly appreciated; I carefully consider every piece of user feedback, and always respond promptly. Specifically, I encourage you to openly share any challenges or negative experiences you encounter during installation or usage. Asking your questions on the public 3DNA Forum benefits not only yourself but also the wider user community.

Enclosed below is the Registration Agreement for the Forum

This forum is dedicated to topics generally related to the X3DNA-DSSR resource for the analysis, rebuilding, and visualization of 3D nucleic acid structures. To make the Forum a pleasant virtual community for all of us to learn from and contribute to, please be considerate and practice good netiquette (http://www.albion.com/netiquette/). See also the FAQ entry "How to make the best use of the Forum".

I strive to make the Forum spam free. Private emails (gmail.com, yahoo.com, qq.com, rambler.ru etc.) are not accepted; such registrations will be removed. Approved registrations that are not activated via email will be deleted. Activated accounts that are not accessed (logins) will be erased. Posts that are not 3DNA/DSSR related in the broad sense are taken as spams and are strictly forbidden. All administrative actions are performed without notification.

DSSR has completely superseded 3DNA (which is still maintained, but no new features other than bug fixes). DSSR integrates the disparate programs of 3DNA under one umbrella, and offers new advanced features, through a convenient interface. DSSR requires no set up or configuration: it just works. See the Overview Video and User Manual.

When posting on the Forum, please abide by the following rules:

0.  Do your homework; read the FAQ and browse the Forum.
1.  Ask your questions on the *public* 3DNA Forum instead of sending
        xiangjun emails or personal messages. Additionally, please note
        that your posts on the 3DNA Forum are in the *public domain*.
2.  Be specific with your questions; provide a minimal, reproducible
        example if possible; use attachments where appropriate.
3.  Respond to requests for clarification. Failure to do so may result in
        delay or no answer to your questions.
4.  Summarize the solution to your problem from a user's perspective
        by providing step-by-step details, for the community's benefit.
5+ Contribute back to the 3DNA project:
        o Report bugs — including typos
        o Make constructive suggestions — anything that can make 3DNA better
        o Answer other users' questions
        o Share your use cases in the "Users' contributions" section

In a nutshell, you are welcome to participate and should not hesitate to ask questions, but remember to play nice and preferably share what you learned! Please note that we do *not* tolerate spamming or off-topic trolling of any form.

60

Site announcements / Re: Download instructions

« Last post by xiangjun on April 19, 2025, 10:06:06 pm »

Only 3DNA v2.4.8-2023nov10 is available for download. The ANSI C source code and Ruby scripts are included in the package, along with precompiled binaries for Linux and macOS. The Linux version should also work under Windows using WSL2. In any case, you can compile the source code easily as long as you have a C compiler installed on your system.