Recent Posts

71

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

« Last post by Sunera on January 30, 2025, 12:51:31 am »

Is it possible to generate a PDB of a single stranded DNA containing a 3-methylated cytosine using the 3DNA Web Server? Could you please advise on the best way to generate an all-atom PDB containing this modification if it cannot be generated using 3DNA?

72

MD simulations / Re: overwritten output files

« Last post by xiangjun on January 13, 2025, 10:47:57 am »

Hi Mamta,

The output file name is derived from the input PDB filename, by deleting extension and add ".out". Since your PDB frame is named "output-filename.pdb.${i}", the output file will always be "output-filename.pdb.out" by replacing ".{i}" with ".out". You could name your PDB frame "output-${i}.pdb" and the corresponding output file will be "output-${i}.out".

Have a look of the C source code, and the x3dna_ensemble script (x3dna_ensemble analyze -h). Overall, the x3dna-v2.4 support for MD analysis is limited. There is also do_x3dna -- I'm not sure if it is still actively maintained.

I'm in the process of incorporating x3dna-v2.4 features into DSSR (Free academic license available from CTV). Further improvement for MD support will be implemented in DSSR.

Best regards,

Xiang-Jun

73

MD simulations / Re: overwritten output files

« Last post by Mamta on January 13, 2025, 10:00:17 am »

Hi Xian- Jung,
thanks for your quick response.
I use the simple script of 3dna -
 for i in $(seq 1 3700); do
    find_pair output-filename.pdb.${i} frame${i}.bps
    analyze frame${i}.bps
done

Thanks
Mamta

74

MD simulations / Re: overwritten output files

« Last post by xiangjun on January 13, 2025, 08:30:07 am »

Hi Mamta,

Thanks for using 3DNA/DSSR and for posting your question on the 3DNA Forum. Could you please be specific with the command you used? The x3dna-v2.4 suite comes with a Ruby script 'x3dna_ensemble' for analyzing MODEL/ENDMDL delineated ensemble of NMR or MD structures. The x3dna-dssr program has an --nmr (--md) option that streamline the analysis of such ensembles.

Best regards,

Xiang-Jun

75

MD simulations / overwritten output files

« Last post by Mamta on January 13, 2025, 04:52:30 am »

Dear all,
I am analyzing the helical parameters of DNA using 3700 frames from my MD simulation, with each frame having a corresponding `.bps` file. When using a `for` loop with the `analyze` command, the output is being overwritten instead of being saved in separate files for each frame.I am using x3dna-v2.4 version. Is it possible to configure the program so that it records the data for all frames without overwriting the output?                                                                                                              Thanks for your help!
Mamta

76

RNA structures (DSSR) / Re: DNA bend angle

« Last post by xiangjun on December 30, 2024, 10:49:36 pm »

Hi Narendra,

Thanks for using DSSR and for posting your question on the 3DNA Forum. Regarding DNA bending angle in 3DNA/DSSR, please refer to the FAQ How to calculate DNA bending angle?. With DSSR, the helical axis info is available with the --more option. See the step-by-step procedures for reproducing Figure 2 -- analysis of the yeast phenylalanine tRNA (1ehz) of the 2015 DSSR paper in NAR.

For your specific example of 1fjl, DSSR readily identifies a helix (stem) with details on the helical axis. However, DSSR does not directly provide you a bending angle for reason given in the above mentioned FAQ.

Best regards,

Xiang-Jun

77

RNA structures (DSSR) / DNA bend angle

« Last post by narayana on December 30, 2024, 09:18:28 pm »

Dear Dr. Lu,

Is there a way to compute bending angle using DSSR program. From your manual I do note that it is possible, but I am not sure how I can specify to do this. For example, for 1fjl, what would be the command line instructions? Your suggestion is much appreciated.

Thank you.

Narendra

78

Site announcements / DSSR-PyMOL enabled schematics on the covers of the RNA Journal

« Last post by xiangjun on December 16, 2024, 04:11:24 pm »

Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

See the 2020 paper titled "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL" in Nucleic Acids Research and the corresponding Supplemental PDF for details. Many thanks to Drs. Wilma Olson and Cathy Lawson for their help in the preparation of the illustrations.


June 2025 (link to the source)

Structure of a group II intron ribonucleoprotein in the pre-ligation state (PDB id: 8T2R; Xu L, Liu T, Chung K, Pyle AM. 2023. Structural insights into intron catalysis and dynamics during splicing. Nature 624: 682–688). The pre-ligation complex of the Agathobacter rectalis group II intron reverse transcriptase/maturase with intron and 5′-exon RNAs makes it possible to construct a picture of the splicing active site. The intron is depicted by a green ribbon, with bases and Watson-Crick base pairs represented as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; the 5′-exon is shown by white spheres and the protein by a gold ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

May 2025 (link to the source)

Complex of terminal uridylyltransferase 7 (TUT7) with pre-miRNA and Lin28A (PDB id: 8OPT; Yi G, Ye M, Carrique L, El-Sagheer A, Brown T, Norbury CJ, Zhang P, Gilbert RJ. 2024. Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs. Nat Struct Mol Biol 31: 1426–1438). The RNA-binding pluripotency factor LIN28A invades and melts the RNA and affects the mechanism of action of the TUT7 enzyme. The RNA backbone is depicted by a red ribbon, with bases and Watson-Crick base pairs represented as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; TUT7 is represented by a gold ribbon and LIN28A by a white ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

April 2025 (link to the source)

Cryo-EM structure of the pre-B complex (PDB id: 8QP8; Zhang Z, Kumar V, Dybkov O, Will CL, Zhong J, Ludwig SE, Urlaub H, Kastner B, Stark H, Lührmann R. 2024. Structural insights into the cross-exon to cross-intron spliceosome switch. Nature 630: 1012–1019). The pre-B complex is thought to be critical in the regulation of splicing reactions. Its structure suggests how the cross-exon and cross-intron spliceosome assembly pathways converge. The U4, U5, and U6 snRNA backbones are depicted respectively by blue, green, and red ribbons, with bases and Watson-Crick base pairs shown as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; the proteins are represented by gold ribbons. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

February 2025 (link to the source)

Structure of the Hendra henipavirus (HeV) nucleoprotein (N) protein-RNA double-ring assembly (PDB id: 8C4H; Passchier TC, White JB, Maskell DP, Byrne MJ, Ranson NA, Edwards TA, Barr JN. 2024. The cryoEM structure of the Hendra henipavirus nucleoprotein reveals insights into paramyxoviral nucleocapsid architectures. Sci Rep 14: 14099). The HeV N protein adopts a bi-lobed fold, where the N- and C-terminal globular domains are bisected by an RNA binding cleft. Neighboring N proteins assemble laterally and completely encapsidate the viral genomic and antigenomic RNAs. The two RNAs are depicted by green and red ribbons. The U bases of the poly(U) model are shown as cyan blocks. Proteins are represented as semitransparent gold ribbons. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

January 2025 (link to the source)

Structure of the helicase and C-terminal domains of Dicer-related helicase-1 (DRH-1) bound to dsRNA (PDB id: 8T5S; Consalvo CD, Aderounmu AM, Donelick HM, Aruscavage PJ, Eckert DM, Shen PS, Bass BL. 2024. Caenorhabditis elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA. eLife 13: RP93979). Cryo-EM structures of Dicer-1 in complex with DRH-1, RNAi deficient-4 (RDE-4), and dsRNA provide mechanistic insights into how these three proteins cooperate in antiviral defense. The dsRNA backbone is depicted by green and red ribbons. The U-A pairs of the poly(A)·poly(U) model are shown as long rectangular cyan blocks, with minor-groove edges colored white. The ADP ligand is represented by a red block and the protein by a gold ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

How are the detailed steps used to generate the above cover image, using DSSR v2.4.6-2024nov15:

Code: Bash

1. # Download the PDB structure in cif format from RCSB
2. wget https://files.rcsb.org/download/8t5s-assembly1.cif -O 8t5s.cif
3.  
4. # Run DSSR with the following settings. See below for file "8t5s-specific.pml"
5. x3dna-dssr -i=8t5s.cif \
6.            --blocview=png-session-black \
7.            --block-file=wc-g4 \
8.            --block-depth=1.0 \
9.            --pymol-ray-size=5000 \
10.            --pymol-aa-color=gold \
11.            --block_color="minor:white" \
12.            --cartoon-cmd-file=8t5s-specific.pml \
13.            -o=8t5s.pml
14.  
15. # Run PyMOL to render the image. Here it is from the command line.
16. # You can also load the 8t5s.pml into PyMOL interactively.
17. # Generate file "8t5s-pymol.png"
18. pymol -Qkc 8t5s.pml
19.  
20. # Use ImageMagick to trim extra margins
21. magick 8t5s-pymol.png -trim +repage -bordercolor black -border 120 8t5s.png

Note the setting of black background, and coloring of minor-groove edge in white. By default, DSSR-PyMOL renders with a white background and black minor-groove edges, as in 8t5s. Whenever feasible, I've integrated features into DSSR to automate routine tasks as much as possible.

Here are the related files:

• 8t5s-specific.pml -- specific settings
• 8t5s.pse -- PyMOL session file
• 8t5s.pml -- PyMOL script file
• -- ray-traced image

Moreover, the following 30 [12(2021) + 12(2022) + 6(2023)] cover images of the RNA Journal were generated by the NAKB (nakb.org).

Cover image provided by the Nucleic Acid Database (NDB)/Nucleic Acid Knowledgebase (NAKB; nakb.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

79

FAQs / Re: How to set up 3DNA on Windows with WSL2

« Last post by nat520 on December 14, 2024, 10:17:54 am »

Dear Dr. Lu,

I am onboard!!!

I have actually set up WSL on my laptop a very long time ago. So I've saved all the installation parts for the WSL2.

I installed the tarball file named x3dna-v2.4-linux-64bit.tar.gz. and moved it to the home directory for my WSL linux.

Then I opened up the WSL2 command prompt and followed the download instructions for linux.

I installed ruby by entering "sudo apt install ruby" in the WSL linux command prompt, but encountered some issues regarding error 404, but it was because my WSL was out of date. This was easily solved by "sudo apt update", followed by repeating the "sudo apt install ruby".

I then continue the download instructions, set up the environment variable X3DNA and add $X3DNA/bin to my command search path.

And finally, find_pair-h works!

Thanks for your prompt reply and suggestion on using WSL2 for running this program! I can start exploring the features and functions of 3DNA whilst waiting for the DSSR license to come through!

Kind Regards,
Chian

80

FAQs / Re: How to set up 3DNA on Windows with WSL2

« Last post by xiangjun on December 14, 2024, 08:41:59 am »

Hi Chian,

Thanks for using 3DNA. Working in native Windows command-line (cmd or PowerShell) has seen lots of troubles, as evidenced from this long thread. I've split the thread so it is easier to see the new posts.

Since you are on Windows 11, please install WSL2 (Window Subsystem for Windows). The default ubuntu system is good to get 3DNA up and running quickly. Please have a try and report back how it goes.

Xiang-Jun