Messages

1

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« on: November 18, 2025, 09:25:57 pm »

Hi Di and Gengshi,

Thanks for the additional information. They are exactly the kind of information I was looking for.

• Glen Report 33-21: L-DNA: Applications and the Recognition of Mirror Image Nucleic Acids
• Structural basis for the targeting of complement anaphylatoxin C5a using a mixed L-RNA/L-DNA aptamer (PDB entry 4WB3)

I'll study them carefully, and try to implement an option in DSSR to handle L-DNA atuomatically. I'll keep you updated.

Best regards,

Xiang-Jun

2

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« on: November 15, 2025, 10:31:55 am »

Hi Gengshi,

Thanks for your clarification regarding the naming of L-DNA, referring to the L-2-deoxyribose. It is a nice coincidence it is also left-handed.

Your L-DNA actually has prompted me to think more about this new (hypothetical) form of DNA, which is left-handed but with a B-type helix, by simply reversing x-coordinates of the classic B-DNA model. I can now have a clear mental image of this L-DNA: left-handed, with base-pairs flipped along the long axis. These are the two key features of Z-DNA, which characterizes a zig-zag backbone of CG repeats. The L-DNA, however, has a smooth backbone, as in B-DNA.

With this knowledge, it is not hard to classify L-DNA automatically with DSSR. I may consider to add the --L-DNA option specifically for this purpose, not to complicate the default DSSR output. It is after all not a common form, as A-, B-, and Z-form DNA. I would to see more examples of such L-DNA.

It is questions like yours that make DSSR more relevant and useful. I always appreciate users' feedback and encourage them to ask questions, sharing their experiences (both good and bad), freely and openly on the 3DNA Forum. Even in the age of AI, I still believe that there is no replacement for the human touch. I watch the 3DNA Forum closely and am quick to respond to users’ questions and concerns.

Best regards,

Xiang-Jun

3

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« on: November 11, 2025, 09:19:56 pm »

Hi Gengshi,

I've checked the two PDB files you uploaded: a standard B-DNA model (ending with aligned2Z.pdb), and its mirror-image (L-DNA), with x-coordinates negated (ending with aligned2Z_i_x.pdb). For clarity, I've extracted the first 6 atoms from each file, so readers easily see the differences.

# a standard B-DNA model          x
ATOM      1  P    DA A   1       0.621   9.421  -1.028  1.00  0.00           P
ATOM      2  O1P  DA A   1       0.606  10.783  -1.583  1.00  0.00           O
ATOM      3  O2P  DA A   1       1.439   9.186   0.166  1.00  0.00           O
ATOM      4  O5'  DA A   1      -0.863   8.945  -0.676  1.00  0.00           O
ATOM      5  C5'  DA A   1      -1.693   8.405  -1.689  1.00  0.00           C
ATOM      6  C4'  DA A   1      -2.528   7.255  -1.154  1.00  0.00           C

# a mirror-image, with x-coordinates negated
ATOM      1  P    DA A   1      -0.621   9.421  -1.028  1.00  0.00           P
ATOM      2  O1P  DA A   1      -0.606  10.783  -1.583  1.00  0.00           O
ATOM      3  O2P  DA A   1      -1.439   9.186   0.166  1.00  0.00           O
ATOM      4  O5'  DA A   1       0.863   8.945  -0.676  1.00  0.00           O
ATOM      5  C5'  DA A   1       1.693   8.405  -1.689  1.00  0.00           C
ATOM      6  C4'  DA A   1       2.528   7.255  -1.154  1.00  0.00           C

Mathematically, this is a simple operation, but you have created a hypothetical DNA type that is unknown to DSSR. Nevertheless, DSSR is functioning as intended:

• For the standard B-DNA model, DSSR classifies the dinucleotide step as 'B' correctly.
• For the L-DNA, DSSR cannot classify the dinucleotide steps. and designates them as '.' (see the section below). Also as noted in the header section, DSSR only recognizes the common A-, B-, and Z-form helices.

  Note: a helix is defined by base-stacking interactions, regardless of bp
        type and backbone connectivity, and may contain more than one stem.
      helix#number[stems-contained] bps=number-of-base-pairs in the helix
      bp-type: '|' for a canonical WC/wobble pair, '.' otherwise
      helix-form: classification of a dinucleotide step comprising the bp
        above the given designation and the bp that follows it. Types
        include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices,
        '.' for an unclassified step, and 'x' for a step without a
        continuous backbone.
      --------------------------------------------------------------------
  helix#1[1] bps=40
      strand-1 5'-AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGG-3'
       bp-type    ||||||||||||||||||||||||||||||||||||||||
      strand-2 3'-TTTTTTTTTTAAAAAAAAAAGGGGGGGGGGCCCCCCCCCC-5'
      helix-form  .......................................

1. Is my understanding correct that DSSR can identify the geometry but does not recognize the form of our L-DNA?

Yes, that is correct. DSSR can see this is a left-handed helix, but it (currently) does not recognize your L-DNA form.

Along the line, one could imagine another form where y-coordinates are flipped. What would it be called? How would DSSR suppose to classify it?

2. Is there any way to make DSSR recognize the form of our L-DNA?

In principle, yes. One just needs to incorporate the domain-specific knowledge into the DSSR code. I need to know more about your L-DNA before considering how to do that.

Best regards,

Xiang-Jun

4

RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« on: November 11, 2025, 12:41:46 am »

Hi Gengshi,

Thank you for sharing details about your L-DNA structure (mirror image of standard B-DNA). It seems to represent a novel form, and I plan to investigate it further. If feasible, I will update DSSR to accommodate this new form.

Best regards,

Xiang-Jun

5

MD simulations / Re: generate DNA pdb file for Gromacs

« on: September 13, 2025, 11:13:30 am »

Hi Mengyao,

Thanks for posting your question on the 3DNA Forum.

We are currently attempting to model non-natural nucleic acid structures. We would like to know if it is possible to predict the structure of threose nucleic acid (TNA). Is this feature already included in some of the tools ?

The main difference between TNA and DNA or RNA lies in the ribose. It is known that DNA (RNA) contains a pentose sugar, while TNA contains a tetrose sugar. Therefore, the connection sites of the phosphodiester bonds are different.

I am not familiar with TNA. From your description, TNA is a non-natural nucleic acid structure with a tetrose, instead of pentose, sugar. Given further information about TNA, I may be able to help build a model as a starting structure for MD simulations.

Best regards,

Xiang-Jun

6

MD simulations / Re: generate DNA pdb file for Gromacs

« on: September 13, 2025, 11:04:50 am »

The DNA pdb file generated by X3DNA has only A T C G, but no terminal base, e.g. A3, A5, T3, T5, ...
How to use X3DNA generate a pdb file with terminal bases?

DSSR has superseded X3DNA, and it can be used to generate a PDB file with terminal bases as you requested. See the following example:

Code: [Select]

# Generate a regular B-DNA model with sequence (AAAAAATTTTTT; shortened as A6T6)
x3dna-dssr fiber --b-dna --seq=A6T6 -o=A6T6-BDNA.pdb

# Mutate residue name 5'-A on chains A and B from the detault 'A' to 'A5':
x3dna-dssr mutate --entry='num=1 to=A5' -i=A6T6-BDNA.pdb -o=A5-both.pdb
A portion of the output PDB file A5-both.pdb is shown below:

REMARK PDB mutated using DSSR
REMARK DSSR mutate: A.A1 to A5
ATOM      1  P    A5 A   1      -0.356   9.218   1.848  1.00  0.00           P
ATOM      2  OP1  A5 A   1      -0.311  10.489   2.605  1.00  0.00           O
ATOM      3  OP2  A5 A   1      -1.334   9.156   0.740  1.00  0.00           O
ATOM      4  O5'  A5 A   1       1.105   8.869   1.295  1.00  0.00           O
ATOM      5  C5'  A5 A   1       2.021   8.156   2.146  1.00  0.00           C
ATOM      6  C4'  A5 A   1       2.726   7.072   1.355  1.00  0.00           C
ATOM      7  O4'  A5 A   1       1.986   5.817   1.352  1.00  0.00           O
ATOM      8  C3'  A5 A   1       2.952   7.370  -0.127  1.00  0.00           C
ATOM      9  O3'  A5 A   1       4.210   6.832  -0.518  1.00  0.00           O
ATOM     10  C2'  A5 A   1       1.848   6.598  -0.850  1.00  0.00           C
ATOM     11  C1'  A5 A   1       1.913   5.344   0.016  1.00  0.00           C
ATOM     12  N9   A5 A   1       0.717   4.478  -0.101  1.00  0.00           N
ATOM     13  C8   A5 A   1      -0.592   4.850  -0.293  1.00  0.00           C
ATOM     14  N7   A5 A   1      -1.424   3.839  -0.355  1.00  0.00           N
ATOM     15  C5   A5 A   1      -0.609   2.726  -0.193  1.00  0.00           C
ATOM     16  C6   A5 A   1      -0.886   1.349  -0.163  1.00  0.00           C
ATOM     17  N6   A5 A   1      -2.111   0.835  -0.301  1.00  0.00           N
ATOM     18  N1   A5 A   1       0.154   0.505   0.016  1.00  0.00           N
ATOM     19  C2   A5 A   1       1.380   1.020   0.154  1.00  0.00           C
ATOM     20  N3   A5 A   1       1.767   2.294   0.144  1.00  0.00           N
ATOM     21  C4   A5 A   1       0.712   3.105  -0.035  1.00  0.00           C
ATOM     22  P     A A   2       5.130   7.667  -1.527  1.00  0.00           P
ATOM     23  OP1   A A   2       5.914   8.669  -0.770  1.00  0.00           O
ATOM     24  OP2   A A   2       4.303   8.192  -2.635  1.00  0.00           O

In addition to the above question, is it possible to generate a pdb file that is fully compatible with Gromacs. Now there are some incompatible things. Such as Gromacs using DA, DT, DC, DG, rather than A, T, C, G.

I'm not sure the exact requirements for compatibility with Gromacs, but you can easily mutate 'A' to 'DA' etc using DSSR mutate subcommand as shown below:

Code: [Select]

x3dna-dssr mutate --entry='A:DA;T:DT' -i=A6T6-BDNA.pdb -o=DA-DT.pdb
See the DSSR User manual for more details.

7

MD simulations / Re: generate DNA pdb file for Gromacs

« on: September 13, 2025, 10:45:00 am »

Would you mind explaining to me how did you generate pdb file for your DNA sequence. I am new to this and stuck now on creating pdb file for my MD simulation. I will appreciate any kind of help here.

With DSSR (here v2.6.0-2025jul24 is used), you can use the following command to generate a PDB file for your (DNA) sequence:

Code: Bash

1. x3dna-dssr fiber --seq= A6C10 --repeat =2 --model =RNA
2. x3dna-dssr fiber --rna -o=rna -ss.pdb
3. x3dna-dssr fiber --rna -ds -o=rna - duplex .pdb # --rna -double , --RNA - duplex
4. x3dna-dssr fiber --g4 -o=g4.pdb
5.  
6. # The following four commands lead to the same results
7. x3dna-dssr fiber --seq= A6TC9 --repeat =2 -o=B1.pdb
8. x3dna-dssr fiber --B-DNA --seq= A6TC9 --repeat =2 -o=B2.pdb
9. x3dna-dssr fiber --model =b-dna --seq= A6TC9 --repeat =2 -o=B3.pdb
10. x3dna-dssr fiber --model =b-dna --seq=A6 -T-C9 --repeat =2 -o=B4.pdb
11.  
12. x3dna-dssr fiber --seq= A1000 --mmcif - output # B-DNA , in mmCIF output format
13.  
14. x3dna-dssr fiber --pauling --seq=A6 # three strands , all A6
15. x3dna-dssr fiber --pauling --seq=C6: # one strand : C6 ( A )
16. x3dna-dssr fiber --pauling --seq=A6:G2 # two strands : A6 ( A ) and G2 ( B )
17. x3dna-dssr fiber --pauling --seq=A6 :: G2 # two strands : A6 ( A ) and G2 ( C )
18. x3dna-dssr fiber --pauling --seq =: U3:G2 # two strands : U3 ( B ) and G2 ( C )
19. x3dna-dssr fiber --pauling -dna --seq=U8 --repeat =4 # U converted to T

See the DSSR User Manual, especially Section "5.2 Regular helical models (fiber)" for more details.

8

RNA structures (DSSR) / Re: Question about axis tilt after reconstruction of B-DNA using x3dna-dssr

« on: August 01, 2025, 09:03:27 pm »

Is there a way to directly generate a -fiber DNA helix with 10.5 bp/turn aligned to the Z-axis, avoiding parameter extraction and rebuilding?

The fiber model is based on experimental data, the details can be found via the following command: x3dna-dssr fiber --list

So the answer is NO with 3DNA/DSSR.

Best regards,

Xiang-Jun

9

RNA structures (DSSR) / Re: Question about axis tilt after reconstruction of B-DNA using x3dna-dssr

« on: August 01, 2025, 11:47:34 am »

Hi Gengshi,

Thanks for using DSSR and for posting your well-formulated question on the 3DNA Forum.

Could you please advise whether this tilt is expected due to reconstruction? Or is there a recommended way to maintain the original axis alignment during rebuilding?

Yes, the rebuilt structure and the original structure are in different coordinate systems, as expected. More specifically, the rebuilt structure is in the reference frame of the first base pair, while the original structure is in a whatever coordinate system it was originally in. For the fiber models from 3DNA/DSSR, base pairs grow from top to bottom, with decreasing z-coordinates. You can easily see this by looking at the dssr-B-DNA-A36.pdb file.

To put the two structures in the same coordinate system, you can use the --frame option of DSSR. Using your example, the command would be:

Code: Bash

1. # dssr-B-DNA-A36.pdb is the coordinate file from DSSR fiber model
2. x3dna-dssr -i=dssr-B-DNA-A36.pdb --frame=A.1:wc -o=expt-ref1.pdb

Now expt-ref1.pdb and the rebuilt structure dssr-B-DNA-A36-rb10.5.pdb would be in the same coordinate system. This is the simplest way to align the two structures. See the DSSR User Manual for more details.

It is also possible to transform the rebuild structure into the coordinate system of the original structure. It is a bit more complicated. I will consider write a blog post on this topic in the future.

You can easily verify that rebuild structure and the original structure are indeed very similar in two ways: One way is to re-analyze the rebuilt structure with DSSR, you will see that the base-pair parameters are very close to the ones for the original structure. The other way is perform a superimposition of the two structures, and  you will see that the RMSD for the base atoms is close to 0. See the commands below:

Code: [Select]

# extract base atoms from the original structure
x3dna-dssr -i=dssr-B-DNA-A36.pdb --select-base -o=exp-base.pdb

# extract base atoms from the rebuilt structure
x3dna-dssr -i=dssr-B-DNA-A36-rb10.5.pdb --select-base -o=rebuild-base.pdb

# the RMSD between exp-base.pdb and rebuild-base.pdb is 0.016.
For your verification, exp-base.pdb and rebuild-base.pdb are attached to this post.

While we're at it, here's an excerpt worth taking from the DSSR User Manual (5.3 Customized structures):

The 3DNA rebuild program complements analyze by reinforcing and verifying it. These two programs are a defining feature of 3DNA (Lu and Olson, 2003, 2008; Li et al., 2019). The 3DNA analyze and rebuild programs are based on SCHNAaP/SCHNArP (Lu et al., 1997a,b) which implement and extend the rigorous CEHS algorithm (El Hassan and Calladine, 1995) for the analysis/rebuilding of DNA duplexes.

The reversibility of the analysis/rebuilding programs in 3DNA allows scientists to ask what-if questions. By first deriving a complete set of base-pair parameters from an experimental structure, they can then systematically introduce changes in these parameters to see what happens to the shapes of the resulting 3D structures. This is a simple, yet powerful concept. 3DNA is the only widely used DNA/RNA structural bioinformatics tool with this feature. It has led to the discovery of a novel roll-and-slide mechanism to account for DNA folding in chromatin (Tolstorukov et al., 2007). Using modeling studies enabled by 3DNA, the Johnson lab at UCLA has revealed slide as a key parameter (along with roll and twist) in mediating DNA minor groove width (Hancock et al., 2019; Chen et al., 2018; Hancock et al., 2016, 2013; Stella et al., 2010).

The DSSR analyze module has completely surpassed the 3DNA analyze program (see Section 3.18). Similarly, the rebuild module in DSSR replaces the 3DNA rebuild program, with enriched functionality and improved usability. The module must be run as x3dna-dssr rebuild, just like a sub-command in Git.

10

General discussions (Q&As) / Re: Download error for 3DNA v2.4.8-2023nov10 C Source Code

« on: July 27, 2025, 04:48:46 pm »

Hi Arman Alborzi,

Thank you for reporting this issue, which has now been resolved. I am currently in the process of updating and reorganizing resources on our servers, which may cause temporary disruptions. Please try again and let me know if the problem persists.

Best regards,

Xiang-Jun

11

General discussions (Q&As) / Re: Rebuild B-DNA

« on: July 25, 2025, 11:33:04 am »

The thymine base in DNA features a methyl group at the C5 position, previously designated as C5M. The updated convention now refers to this as C7. DSSR v2.6.0, available on the CTV download page, has renamed the thymine methyl group at the C5 position from C5M to C7. This revision ensures that DSSR's atomic model rebuilding aligns with the current nomenclature.

The make this response complete, here are the DSSR commands for generating the B-DNA model based on PDB entry 1hlo:

Code: Bash

1. # Verify DSSR version
2. x3dna-dssr -v
3.       # v2.6.0-2025jul24
4.  
5. # PDB file 1hlo.pdb is downloaded from RCSB PDB
6. x3dna-dssr analyze --input=1hlo.pdb --rebuild-parameters
7.  
8. # The above command generates file dssr-dsStepPars.txt
9. x3dna-dssr rebuild --backbone=B-DNA --par-file=dssr-dsStepPars.txt --o=new2.pdb

Attachments:

• dssr-dsStepPars.txt
• new2.pdb

12

Bug reports / Re: When analyzing multiple frames with --nmr, DSSR gets slower with each frame

« on: July 23, 2025, 11:29:24 pm »

I have updated DSSR Academic to version 2.6.0, which significantly speeds up the analysis of multiple frames of MD trajectories. The default settings will no longer experience slowdowns with later frames. The runtime should now scale linearly with the number of frames, as expected.

The new DSSR Academic v2.6.0 will shortly be available on the CTV download page, expected to be released within the next few days.

Note added on 2025-07-25: DSSR v2.6.0 is now available on CTV download page

13

DNA/RNA-protein interactions (SNAP) / Re: Implement Json

« on: July 23, 2025, 11:12:13 pm »

As a follow up of the previous response, I would like to let the community know that as of DSSR Academic v2.6.0, the `--json` option is available for the SNAP subcommand. The new DSSR Academic v2.6.0 should be available in the CTV download page soon (in the next few days).

Note added on 2025-07-25: DSSR v2.6.0 is now available on CTV download page

14

General discussions (Q&As) / Re: Rebuild B-DNA

« on: July 06, 2025, 10:41:34 am »

Thanks for your feedback.

I've revised DSSR to replace C5M with C7 for thymine in A- and B-DNA. See the attached `new2.pdb` file.

As a side note, you could use the following command with the DSSR version you currently have installed:

Code: [Select]

x3dna-dssr mutate -i=new.pdb --entry='name=T to=T' -o=newx.pdb
Basically, it mutats T to T using the `mutate` subcommand. The net effect is C5M being replaced with C7 (see attached).

Best regards,

Xiang-Jun

15

General discussions (Q&As) / Re: Rebuild B-DNA

« on: July 05, 2025, 11:14:02 pm »

Hi,

Thanks for using DSSR and for posting your question on the Forum. The two DSSR commands you used help illuminate the question well, and the snippets from your `new.pdb` file clearly show the issue.

However, I noticed that in the rebuilt DNA structure (new.pdb), all thymine bases appear to be methylated—specifically, the C5M atom shows up in the output. There is no methylation in my initial input file(1hlo.pdb)

The thymine base in DNA has a methyl group at the C5 position, which is named differently across various versions of the PDB
format. Historically, it was referred to as C5M, but in more recent versions (e.g., in `1hlo`), it is labeled as C7. For further
details, please refer to my blog post titled "Different names for the methyl group in DNA and RNA structures" at
https://x3dna.org/articles/different-names-for-the-methyl-group-in-dna-and-rna-structures

The presence of `C5M` in your `new.pdb` is because the building block in DSSR currently uses `C5M` to denote the methyl group on thymine instead of `C7`. Since you raised this point, I am considering updating DSSR to use `C7` for thymine in future versions. In the meantime, you can simply replace `C5M` with `C7` in your `new.pdb` file.

Best regads,

Xiang-Jun

16

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

« on: June 20, 2025, 10:56:12 am »

Hi,

Thanks for posting back and following up on the question about modeling G-quadruplexes. As mentioned in my May 05 post, G4 modeling are "experimental (and undocumented) features" in DSSR, and need to be further developed. DSSR is not open-source, and the Columbia Technologies Ventures (CTV) is in charge of licensing the command-line version of DSSR.

Best regards,

Xiang-Jun

17

DNA/RNA-protein interactions (SNAP) / Re: Implement Json

« on: June 13, 2025, 04:19:01 pm »

Hi,

Thanks for using SNAP/DSSR and for posting your question on the Forum.

The --json option is available in the DSSR Pro version (x3dna-dssr snap --json) . This is one of the few features that is currently not enabled in the free DSSR Basic Academic version. No paper on SNAP has been published yet. Some features need further developments and better documentation. I may consider enable more Pro features in the Basic version in the future.

The general principle of 3DNA/DSSR is to ensure that published results and documented features (in the DSSR Manual) are reproducible. DSSR has more to offer than those published/documented.

Best regards,

Xiang-Jun

18

Bug reports / Re: When analyzing multiple frames with --nmr, DSSR gets slower with each frame

« on: June 13, 2025, 10:36:42 am »

It sounds like a good suggestion. I will think about it.

19

RNA structures (DSSR) / Re: Using --helical-axis with the --nmr option in DSSR

« on: June 12, 2025, 02:57:39 pm »

Hi,

Thanks for your kind words about DSSR. Please try the --more option which will output "helical-axis", "point-one" and "point-one" as documented in the DSSR User Manual. You could parse the corresponding output for each model and start from there to calculate the bending angle.

Hope this helps.

Xiang-Jun

20

Bug reports / Re: When analyzing multiple frames with --nmr, DSSR gets slower with each frame

« on: June 12, 2025, 02:51:55 pm »

Hi,

Thanks for using DSSR and for posting your question on the Forum. I am aware of the issue you are describing. The initial design of the --nmr option allows for flexibility of user-selected frames/models (e.g., --nmr=3+5+6:9 as described in the User Manual). For each frame/model, DSSR re-reads the input file from the beginning, which causes the slowdown as you observed. There is no memory leak, as you can verify with valgrind or similar tools.

DSSR Pro version allows for sequential processing of all the frames in a single pass, which leads to faster performance (scale linearly with the number of frames).

Best regards,

Xiang-Jun

21

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

« on: June 03, 2025, 12:42:43 am »

Hi Di,

Thanks for sharing the detailed steps you used to build the Z-DNA circle. What you called Y-shift and Z-shift are Slide and Rise, respectively, in the literature. Slide is an important parameter in determining DNA shapes, see "A Novel Roll-and-Slide Mechanism of DNA Folding in Chromatin: Implications for Nucleosome Positioning" and "The shape of the DNA minor groove directs binding by the DNA-bending protein Fis". It is also crucial for producing circular DNA structures, as you noticed.

Given below is the DSSR commands I used to generate the ZDNA-circle.pdb file I posted previously, plus further steps to improve the visualization of the 3D structure.

Code: Bash

1. # The starting point is your twist60-G84-scaled.pdb. Here only G on chain A is selected.
2. x3dna-dssr -i=twist60-G84-scaled.pdb --select-chain=A -o=chainA.pdb
3.  
4. # Extract a GpC step in Z-DNA conformation, and re-orient it in the reference frame of the first G (on Chain A)
5. x3dna-dssr fiber --z-dna --repeat=1 -o=fiber-GpC.pdb
6. x3dna-dssr -i=fiber-GpC.pdb --frame=A.1 -o=frame___Z.pdb
7.  
8. # Now mutate each G to a Z-DNA GpC step (frame___Z.pdb). The --mutate-type option is new in DSSR v2.5.3
9. #      "whole" to include backbone, and "raw-id" to keep the original identification of the atoms
10. x3dna-dssr mutate -i=chainA.pdb --entry="name=G to=Z" -o=ZDNA-circle.pdb --mutate-type=whole-raw-id
11.  
12. # The following steps would lead to better visualization of 3D structures
13. x3dna-dssr --order-residue -i=ZDNA-circle.pdb -o=temp_order.pdb --po-bond=3.6
14. x3dna-dssr --renumber-residue -i=temp_order.pdb -o=temp_renum.pdb
15. x3dna-dssr --connect-file -i=temp_renum.pdb -o=ZDNA-circle2.pdb --po-bond=3.6

The ZDNA-circle2.pdb and PyMOL-rendered image are attached. For completeness of this post, I have also attached twist60-G84-scaled.pdb from your previous post. With DSSR v2.5.3, users should be able to follow the above steps, and reproduce the results without any issues.

The overall strategy should be clear: in essence, the commands simply replace the 84 Gs with GpC dinucleotides steps in Z-DNA conformation. The method is generally applicable to other DNA/RNA modeling tasks, as demonstrated in my blogpost mentioned earlier "Mutate backbone of DNA and RNA structures". The integrative nature of DSSR is a key strength, and the automation it enables stands out when compared with alternative tools.

There are still areas that require refinement. I am more than willing to enhance the modeling capabilities in future releases of DSSR based on your feedback.

Best regards,

Xiang-Jun

22

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

« on: June 02, 2025, 12:50:18 am »

Hi Di,

Thanks for your confirmation. See my blog post Mutate backbone of DNA and RNA structures. The x3dna-dssr mutate sub command can now mutate a base to another fragment with backbone and/or more than one nucleotides. This make it a generally applicable modeling tool within DSSR.

I will post details on how the circular Z-DNA was generated in the next couple of days. We can polish the procedure together to better fit your needs, and hopefully it would be useful to other users as well.

Best regards,

Xiang-Jun

23

RNA structures (DSSR) / Re: License requested

« on: May 31, 2025, 11:40:43 am »

Hi,

Thanks for your interest in DSSR, and for posting on this forum. I am aware of the issue, and put the following note in the Download instructions.

DSSR v1.9.10-2020apr23 --- This version corresponds to the paper "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL" (2020) in Nucleic Acids Research. From version 2.0 (released around the summer of 2020), DSSR has been licensed by the Columbia Technology Ventures (CTV), who manages the free DSSR Academic licenses as well as paid DSSR Pro licenses for both academic and commercial users. I've lately learned of academic users from certain countries having trouble in getting DSSR Academic licenses. This pre-licensed version is provided (as is) here to fill the gap: it is slightly outdated but still works well. Whenever possible, however, users should obtain the latest version of DSSR through CTV --- it is free for academic uses and fully supported by the NIH R24GM153869 grant.

Best regards,

Xiang-Jun

24

MD simulations / Re: Base pair number not staying constant in simulations

« on: May 21, 2025, 10:03:01 am »

Thanks for the detailed report. While @rkumar should be the primary contact for dnaMD related issues, I'd like to address the general question of why the base pair number not staying constant in simulations.

In 3DNA, the find_pair program is used to identify base pairs in an input structure. For MD trajectories, when each frame is processed with auto-detected base pairs, the numbers can fluctuate due to the dynamic nature of the system. The 3DNA suite includes the Ruby script x3dna_ensemble, and the beginning portion of the "x3dna_ensemble analyze -h" command is as follows. Basically, it requires a template base-pair input file, possibly generated with ‘find_pair’ and manually edited as necessary.

------------------------------------------------------------------------
Analyze a MODEL/ENDMDL delineated ensemble of NMR structures or MD
trajectories. All models must correspond to different conformations
of the same molecule. For the analysis of duplexes (default), a template
base-pair input file, generated with 'find_pair' and manually edited
as necessary, must be provided.

Usage:
        x3dna_ensemble analyze options
Examples:
        x3dna_ensemble analyze -b bpfile.dat -e sample_md0.pdb

In DSSR, the --nmr (or --md) option can be used with --pair-list-input to analyze MD trajectories with a customized set of base pairs of interest. See the DSSR User Manual for more details in Sections "3.13 The --nmr option" and "3.9 The --pair-list options".

Best regards,

Xiang-Jun

25

MD simulations / Re: Do I need gromacs to use dnaMD for simulations?

« on: May 16, 2025, 10:00:09 am »

Thanks for the x3DNA-DSSR software which works wonderfully for single PDBs.

Thanks for using DSSR and for posting your questions on the 3DNA Forum. As for the analysis of an ensemble, please see the DSSR manual , especially Section: "3.13 The --nmr option":

The DSSR --nmr (or --md) option automates the analysis of an ensemble, such as NMR structures in the PDB or snapshots from MD simulations. The input coordinates file must be in either the classic PDB format where each model is delineated by MODEL/ENDMDL tags, or the mmCIF format where each ATOM/HETATM record has an associated model number.
...
The --json option makes it easy to parse the output of multiple models pragmatically. In addition to NMR structures, trajectories from MD simulations can also be processed. Popular MD packages (AMBER, GROMACS, CHARMM, etc.) all have their own specialized binary formats for trajectories. By design, DSSR does not work on these binary files. They must be converted to the standard PDB or mmCIF format to be analyzed by DSSR. The combination of --nmr and --json makes DSSR directly accessible to the MD community.

I have some MD simulations I would like to analyze with dnaMD. I ran them with Amber but converted them to GROMACS .xtc + .pdb files for analysis.

Do I need GROMACS version of dnaMD to analyze simulations or can I use the Python module of dnaMD without GROMACS for simulations?

I am not a practitioner of MD simulations. Questions related to dnaMD are best answered by its developer: hopefully @rkumar will chime in. See the thread Update of do_x3dna package, which can be used with files generated by GROMACS.

PS. I am also lacking the link to download the 3DNA from the forum for some reason, my forum view is similar to unregistered users.

There have been too many spam registrations nowadays, so I must stay continuously vigilant to keep the Forum clean. You should now see the download link. Sorry for the inconvenience.

Best regards,

Xiang-Jun