Messages

1

RNA structures (DSSR) / Re: Building G-quadruplexes

« on: Today at 02:01:05 pm »

Hi shr,

I've split your response from the thread "Rebuilding circular Z-DNA" into its own thread for better organization and discussion.

It a nice start with the first G-tetrad. Please add more features to your GQ-gen.py script so it can at least build a complete G-quadruplex structure. I'll chime in with some suggestions to your project, while I'm working on adding proper Z-DNA backbone to DSSR-enabled models.

Best regards,

Xiang-Jun

2

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« on: April 25, 2025, 02:34:26 pm »

Hi Di,

Thanks for providing further details on how the structure was generated. Such contextual information is always helpful and serves as a valuable reference for the automated approach we aim to develop.

I will take a closer look at the topic and hopefully could come up something to share by next week. Ad hoc solution is easier to implement but I am keen for a systematic approach as mentioned briefly in my previous response.

Best regards,

Xiang-Jun

3

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« on: April 25, 2025, 07:40:54 am »

Hi Di,

This looks good. Please provide the commands used to generate the structures, for example, as I did in the blogpost on "Building extended Z-DNA structures with backbones using DSSR". Every detail counts for reproducibility.

Moreover, I would also consider the case where C-G pairs instead of G-C pairs are present in the structure. Or all 168 pairs with CGCG... sequence. I've thought about the case, and I think what we are trying to acheive fit under the general category of mutated backbones, given the atomic coordinates of base atoms. This is in contrast to the mutating bases feature currently implemented in `mutate_bases` in 3DNA and the `x3dna-dssr mutate` subcommand in DSSR.

Best regards,

Xiang-Jun

4

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« on: April 24, 2025, 11:07:20 pm »

Hi @Di_Liu,

I tried to make some progress on constructing a 168-bp circular Z-DNA structure. What I have achieved so far is determining the positions of the repeating units (each being a CG dimer) along the ring. Each position currently serves as a placeholder (a G:C pair; 84 in total), to be replaced by a Z-DNA dimer unit.

I'm attaching a screenshot of the current structure, as well as the corresponding PDB file. I think Xiang-Jun might be able to work his "tasks" magic to align and insert the Z-DNA dimer units into the specified positions.

Nice progress! Using DSSR, I can see clearly the 84 isolated G-C pairs along the circular structure. I will consider adding an option to "x3dna-dssr tasks" subcommand to replace these G-C pairs with GpC dinucleotide steps. Before doing that, it helps to manually replace a few of these G-C pairs with GpC steps to see how the structure looks like. These examples would also server as test cases to validate the new option.

If you think this direction makes sense, I’d be happy to post the detailed process of how I constructed this circle.

Yes, it does make sense. Please go ahead and post the details of your construction process. It may take several iterations to get the desired results. The more concrete our discussions are, the better we can understand each other.

Best regards,

Xiang-Jun

5

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« on: April 24, 2025, 10:50:29 pm »

Hi @shr,

My work focuses on molecular dynamics simulations of Z-DNA and its interactions with binding proteins. I'm particularly interested in understanding the mechanisms that stabilize Z-DNA, which is inherently less stable than B-DNA. To explore this, I used the crystal structure of the ADAR1 protein bound to a short Z-DNA segment. Since the original segment was quite short, I wanted to extend the Z-DNA backbone. With your help, I was able to successfully simulate this extended structure.

Thanks for the background information about your work on Z-DNA structure. I am glad to hear that the extended Z-DNA structure allowed you to perform your simulations.

However, I encountered challenges in reproducing the specific protein–Z-DNA interactions observed in the crystal structure during my simulations. I believe this is due to multiple non-specific interactions forming between the DNA and the protein, which may mask or override the specific contacts I'm trying to study. It is not a Z-DNA remodeling problem but I am working on understanding Z-DNA stability.

Thank you for sharing your story. Z-DNA modeling is just the first step in understanding its role in biological processes. The other part is beyond the scope of DSSR.

In addition to Z-DNA, I also work on other non-canonical DNA structures, particularly G-quadruplexes (G4s). I’m developing a method to construct ideal G-quadruplex models from sequence data by first arranging guanine bases into tetrads, then building in the backbone and loop regions.

I am glad to hear about your work on G-quadruplexes. Actually, I have recently revised the G4 module in DSSR, fixed existing bugs, and added new features. The g4.x3dna.org website has undergone a complete overhaul, enabling users to upload their own structures for dynamic G4 analysis. Additionally, the DSSR-G4DB database is being actively updated on a weekly basis as new PDB entries are added. See the four blog posts comparing DSSR with other related analysis tools on G-quadruplexes: ASC-G4, Webba da Silva nomenclature, ElTetrado and related tools, and CIIS-GQ.

Moveover, I am also interested in modeling G-quadruplexes, taking G-tetrad as the building block. There are quite a few other threads in DSSR I'd like to pursue further in the future. I'd certainly like to hear more about your approach on modeling G-quadruplex.

As @Di_Liu suggested, I believe a similar model-building strategy could be applied to Z-DNA, to help generate consistent and realistic structures. What do you think about this approach or direction?

Yes, I believe the underlying principles can be generally applicable, including Z-DNA or right-handed A-/B-DNA. The approach in "Building extended Z-DNA structures with backbones using DSSR" is virtually the same as the one used for "create a 26 bp RNA from a 13 bp system".

Please provide more details. Working together with @Di_Liu, we should be able to come up with some interesting results.

Best regards,

Xiang-Jun


Best regards,

Xiang-Jun

6

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

« on: April 24, 2025, 08:30:01 am »

I apologize once again.

I appreciate your attitude and the effort you put into bringing up this interesting topic on the Forum. This case also reminds me that I should be a bit more proactive in engaging with users like you. I always respond directly to users' questions, no matter how minor. Whenever necessary, I ask for clarification to ensure I understand and address their issues correctly. However, if there’s no response, I normally shy away from pushing users further—even though I may have done extra work to make sure I’m on the right track.

I look forward to the blogpost and will check out the thread "Rebuilding circular Z-DNA".

Done. Please see the blogpost Building extended Z-DNA structures with backbones using DSSR. Following the steps in the blogpost, users should be able to build extended Z-DNA structures exactly as described.

I would be happy to contribute in any way I can.

I noticed your follow-up post and the one from @Di_Liu on the new thread Rebuilding circular Z-DNA under the section 'RNA structures (DSSR).' This kind of participation is exactly what I have in mind for the forum. I will get back to you over there soon.

Working together, we should be able to come up with a solution that not only solves the problem at hand but also benefits the community. DSSR would become even more powerful!

Best regards,

Xiang-Jun

7

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

« on: April 22, 2025, 06:17:34 pm »

Hi Di,

Thanks for the detailed response. I can only wish that all users are just like you in providing such helpful feedback. Over the years, it is users like you who have motivated me to keep working on DSSR ...

Best regards,

Xiang-Jun

8

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

« on: April 22, 2025, 12:14:22 pm »

This topic has been moved to RNA structures (DSSR).

http://forum.x3dna.org/index.php?topic=1045.0

9

RNA structures (DSSR) / Re: Rebuilding circular Z-DNA

« on: April 22, 2025, 12:13:54 pm »

Hi Di,

Thanks for chiming in on the topic on modeling Z-DNA structures with proper backbones. User @shr "would also look forward to Z-DNA backbones being included in DSSR modeling functionalities."

Let's continue the discussion through this thread. Your special interest in circular Z-DNA structures will also be taken into account.

In addition to splitting the topic as a new thread, I have also moved the thread under the Section on RNA structures (DSSR) from "General discussions (Q&As)". I aim to develop this feature within DSSR. As noted previously, the classic 3DNA suite of programs has been superseded by DSSR.

If you and @shr could share what you have done so far, I would very much like to see. The more concrete examples, the better.

Best regards,

Xiang-Jun

10

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

« 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

11

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

« 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

12

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

« 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

13

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

« 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

14

Site announcements / On registration and posting

« 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.

15

Site announcements / Re: Download instructions

« 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.

16

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

« on: March 17, 2025, 09:18:59 am »

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.

17

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

« 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).

18

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

« 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

19

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

« on: March 13, 2025, 03:56:04 pm »

Thanks for your quick follow-up.

As noted in the x3dna_utils cp_std -h help message, the utility covers the most common use cases:

Select the standard data files to be used with "analyze" and "rebuild".
Available sets include BDNA, ADNA, NDB96 and RNA, which have exactly
the same base geometry and orientation (in the standard base reference
frame) but different backbone conformations.

Z-DNA is different from the standard right-handed DNA/RNA double helix in that it has not only a left-handed twist but also a base flip, and it has a di-nucleotide (most commonly CpG) as a the building block. So the x3dna_utils cp_std does not cover Z-DNA. However, you can run analyze, modify the output parameters (and extend as needed), and then rebuild a Z-DNA structure according to the modified parameters.

What specific Z-DNA structure you’d like to extend? If you do not want share details, please use a sample Z-DNA structure that helps illustrate your point. Reproducibility is important.

Best regards,

Xiang-Jun

20

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

« on: March 13, 2025, 02:14:06 pm »

Hi,

Thanks for using 3DNA and for posting your questions on the Forum. 3DNA rebuild should be able to build Z-DNA structures given a set of parameters. Please be specific with what you are trying to achieve, and we can start from there.

Best regards,

Xiang-Jun

21

General discussions (Q&As) / Re: Generation of ssDNA PDB with m3C modification using 3DNA webserver

« on: February 28, 2025, 08:47:06 am »

Welcome back.

But I do not have a PDB structure with the m3C modification, I was hoping that we would be able to generate the PDB (and PSF) using 3DNA/DSSR by specifying the residues.

Are you expecting 3DNA/DSSR to "generate the PDB" by specifying the residues, including unknown ones?  3DNA/DSSR can build DNA/RNA structures with standard bases (A,C,G,T,U), or modified ones with *known* building block as illustrated in 5-methylcytosine in the FAQ. It does not generate structures for ligands like m3C. It is up to the user to provide such building blocks for 3DNA/DSSR to proceed. CCP4 and Phenix may have utilities to generate new ligands.

By the way, what does PSF stand for?

As a side question, what would be a good force field that can allow us to perform a phase separation simulation with the methylated ssDNA and IDR sequence?

Sorry, I'm not familiar with this field, and I cannot offer any valuable suggestions. Overall, this question is out of the scope of the Forum.

Best regards,

Xiang-Jun

22

MD simulations / Re: Update of do_x3dna package

« on: February 22, 2025, 11:23:27 pm »

Hi Rajendra,

Thanks for the update to do_x3dna for GROMACS-2025. It is great that the "binary package can be used with files generated by any version of GROMACS". Over the years, I've received emails about applying 3DNA to MD simulations, and I know that your do_x3dna package is well received by the community.

Best regards,

Xiang-Jun

23

General discussions (Q&As) / Re: Opening values and the definition for base-pair parameters

« on: February 07, 2025, 10:22:26 am »

Hi Jing,

Please follow what I suggested in the previous response. As for the 3DNA source code, did you notice the download link at the top and the Download instructions post?

Best regards,

Xiang-Jun

24

General discussions (Q&As) / Re: Opening values and the definition for base-pair parameters

« on: February 06, 2025, 11:14:10 am »

Hi Jing,

I have attached several pictures here. They are G and G pairs. The first two are with the opening \~180, the third picture is with \~-180, and the last two are with \~90.

Thanks for your follow up, and for providing images that illustrate G.G pairs with opening around 180 and 90 degrees. It would have been more helpful if you attached the corresponding PDB files. When posting questions in the future, thinks about providing (mininal) examples so others can *reproduce* the cases.

Now I understand the question you're asking. Let's use a G+G pair in G-tetrad of G-quadruplexes as an example, which has an opening around 90 degrees. Assuming you have downloaded the coordinates file `5ua3.pdb` for PDB entry 5ua3 on "Crystal structure of a DNA G-quadruplex with a cytosine bulge". Please try the following DSSR commands:

Code: [Select]

# This extract DG1 and DG6 from chain A into file 5ua3-GG.pdb
x3dna-dssr -i=5ua3.pdb --select-residue='A 1+6' -o=5ua3-GG.pdb

# Set the pair into the base reference frame of A.DG1
x3dna-dssr -i=5ua3-GG.pdb --frame='A.1' -o=5ua3-GG-frame1.pdb

# Generate the schematic with base blocks
x3dna-dssr -i=5ua3-GG-frame1.pdb --cartoon-block=sticks-label --block-file=slim-outline -o=5ua3-GG-frame1.pml
Load `5ua3-GG-frame1.pml` into PyMOL to see the attached image where the (`slim`) base blocks are nearly perpendicular, corresponding to an opening angle of ~90 degrees.

Analyze `5ua3-GG.pdb` (or `5ua3-GG-frame1.pdb`) with `--more` option to see the six base-pair parameters, including opening.

Code: [Select]

x3dna-dssr -i=5ua3-GG.pdb --more

# With the following detailed information:
List of 1 base pair
     nt1            nt2            bp  name        Saenger   LW   DSSR
   1 A.DG1          A.DG6          G+G --          06-VI     cWH  cW+M
       [-131.0(anti) ~C2'-endo lambda=62.6] [-128.4(anti) ~C2'-endo lambda=28.0]
       d(C1'-C1')=11.59 d(N1-N9)=9.65 d(C6-C8)=9.30 tor(C1'-N1-N9-C1')=10.9
       H-bonds[2]: "N1(imino)-O6(carbonyl)[2.95],N2(amino)-N7[2.91]"
       interBase-angle=1  Simple-bpParams: Shear=-2.67 Stretch=2.83 Buckle=-0.8 Propeller=0.5
       bp-pars: [1.61    3.54    -0.15   0.14    0.94    -89.63]
Note that the opening is reported as `-89.63` --- if you try to align A.DG6 to A.DG1, you need to rotate ~`-90` degrees as can be seen in the attached images. If you swap the pair, the opening would be ~`+90` degrees. See the [2003 3DNA paper in NAR](https://doi.org/10.1093/nar/gkg680), specifically the section "Base pair parameters".

With a clear understand of the above example, you should have little difficult in understanding opening ~180 degrees. You are suggested to follow the above example on one of such cases, and report back your findings.

Note that 3DNA/DSSR report angular parameters in the range of [0, +-180] instead of [0, 360]. So opening of `-175` is not that much a difference from `+175` (vs `+185`). Also notice the opposite sign of opening for M+N vs N+M pairs.

Please read the [DSSR manual](http://docs.x3dna.org/dssr-manual.pdf) and the [practical guide for the DSSR-PyMOL](http://skmatic.x3dna.org/dssr-schematic-guide.pdf) article.

Best regards,

Xiang-Jun

25

General discussions (Q&As) / Re: Opening values and the definition for base-pair parameters

« on: February 03, 2025, 06:05:26 pm »

Hi Jing,

Thanks for using 3DNA, and for posting your questions on the Forum. Your confusions about the details are understandable, and can be clarified most effectively using concrete examples. Do you have examples with opening ~90 and 180?

Since 3DNA source code is available, you can dig into it to see exactly how the base reference frames are defined and how the various parameters are calculated.

Best regards,

Xiang-Jun