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31
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:
Quote
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


32
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!
33
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.
34
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.

35
General discussions (Q&As) / Re: Rebuilding Z-DNA
« Last post by shr on March 17, 2025, 09:21:03 am »
Sorry! I could download it now. It was probably an issue with my browser.
36
General discussions (Q&As) / Re: Rebuilding Z-DNA
« Last post by xiangjun on March 17, 2025, 09:18:59 am »
Quote
But I am unable to properly download the pdb file.

What do you mean? Just click on the link and it should download automatically. I've never heard of any issues with downloading files as long as you have an active internet connection. Please clarify your issue so I can assist you better.


37
General discussions (Q&As) / Re: Rebuilding Z-DNA
« Last post by shr on March 17, 2025, 08:17:00 am »
Thank you so much! But I am unable to properly download the pdb file. I will try to follow the method you mentioned about in your previous reply.
38
General discussions (Q&As) / Re: Rebuilding Z-DNA
« Last post by xiangjun on March 15, 2025, 12:18:44 am »
Does the attached PDB file (with base schematic image) fulfill your needs? The backbone connection between the two segments are a bit longer than normal O--P covalent bond distance, which you can regulated with energy minimizations (e.g., using Phenix, as shown in "Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures" (https://doi.org/10.1093/nar/gkz394).
39
General discussions (Q&As) / Re: Rebuilding Z-DNA
« Last post by xiangjun on March 14, 2025, 08:12:34 am »
Thanks for your follow-up questions and the details you provided. It is always helpful to to be specific when discussing research topics.

Yes, "rebuild -atomic" would have issues with backbone connectivity, since in Z-DNA, nucleotide G is in syn conformation instead of anti (for C). The building block must be adjusted accordingly. I'll look into this further to see what we can get.

Another approach is to take the whole Z-DNA structure as a unit, and perform some transformations to extend it. See the PyMOL thread a few years ago on "create a 26 bp RNA from a 13 bp system" (https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg16190.html). The idea is applicable to Z-DNA as well. Note that the features are now available in the free DSSR Academic license (previously in DSSR Pro Academic only). Check if that method makes sense to you.

Best regards,

Xiang-Jun

40
General discussions (Q&As) / Re: Rebuilding Z-DNA
« Last post by shr on March 14, 2025, 06:05:18 am »
Thank you for your quick responses!
My input structure is the PDB structure 1QBJ. It is a 6nt DNA. I have attached a picture. Without using the x3dna_utils, even without extending, the backbone cannot  be modelled due to the distance of O3' and P being over 4.5 and throws the following error. However, I also tested with the fiber model of Z-DNA to understand how it works with Z-DNA. I found that besides the backbone not being modelled which is because of the PDB dataset not being since I'm not using x3dna_utils, rebuild could model the bases as separate molecules. So, this is possibly the issue with my Z-DNA crystal structure model.

Another observation was, previously, for the crystal structure of BDNA complexed with the protein, I tried to manually extend the DNA in pymol but due to the terminal base positions, I could not properly build the double helix. But after analyze and rebuild, I could. So I assume it is due to standardization of the structure after rebuild. However, there is a problem with this method for Z-DNA. Even if I manage to standardize the structure, pymol does not offer building Z-DNA. So, I was wondering if I could add the extended DNA before rebuild. As you suggested, I modified the bp_step.par file since that is the file used as input for rebuild. Is that the correct way? I apologize if I am asking too many questions.   
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Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University