Recent Posts

31

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.


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).

32

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

33

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

34

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

« Last post by nat520 on December 14, 2024, 06:47:13 am »

Dear Dr. Lu,

I am trying to install x3dna-v2.4 on Windows 11 following the instructions.
However, I still can't execute find_pair -h on ConEmu.
I tried to perform some troubleshooting by looking over similar issues posted on this forum, such as "dir", "echo %X3DNA%", "echo %PATH%" and "dir %X3DNA%config\version".. and all the feedbacks seem alright..
I actually have tried Ruby and Mingw too but that all still didn't work out so in the end i got rid of them.
I have attached the screenshots, can you help on this, where have I missed out?
And I would like to get a confirmation that x3dna-v2.4 does not need a license to download, and working on native window using ConEmu is perfectly alright?

Kind Regards,
Chian

35

FAQs / Re: Running DSSR on macOS

« Last post by xiangjun on November 08, 2024, 09:30:04 pm »

As a follow up, please note that:

The CTV distributes DSSR Basic and Pro versions in zip format for macOS, Linux, and Windows. Each zip file contains a DSSR binary executable as well as the associated user manual.

Assuming basic command-line knowledge, users should be able to follow the instructions in the manual and reproduce reported results.

36

FAQs / Re: Running DSSR on macOS

« Last post by xiangjun on November 08, 2024, 06:46:53 pm »

Thanks for your interest in using DSSR. Your screenshot provides information that explains why you're having problems using DSSR.

You're on a macOS, and you have double-clicked the x3dna-dssr executable to run it. I can reproduce your case by installing x3dna-dssr under the ~/Downloads folder and double-clicking it. The error message is quite informative, by showing that x3dna-dssr is run, and immediately exit. Running x3dna-dssr without any options gives the following message:

missing required option: must specify -i=PDBFile/mmCIF

type: 'x3dna-dssr -h (or --help)' for further help
      'x3dna-dssr --citation' for preferred citation(s)

Time used: 00:00:00:00

That means DSSR is already successfully installed on your macOS. It is just that DSSR is a command-line (CLI) program, and you need a terminal window to run it. There are many online tutorials on how to get started using terminal on macOS. Here is one: Absolute BEGINNER Guide to the Mac OS Terminal. Once you are familiar with the terminal, running DSSR should be straightforward, as detailed in the User Manual.

The DSSR executable (x3dna-dssr for macOS and Linux, and x3dna-dssr.exe for Windows) is self-contained and does not rely on any third-party libraries. There is no need for any setup or configurations: type x3dna-dssr -h to verify your installation. Note that DSSR is a command-line program: you need a terminal window to run it.

If you're GUI-driven and do not want to use CLI at all, then you may find the following two resources helpful:

• DSSR-enabled Innovative Schematics of 3D Nucleic Acid Structures with PyMOL
• Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures

Best regards,

Xiang-Jun

37

FAQs / Running DSSR on macOS

« Last post by lillytishkoff on November 08, 2024, 01:36:12 am »

DSSR Download Issue

 received a license approval to download DSSR- Basic and when I downloaded, I received an error. The software is still not working (see screenshot). Please advise how I can fix.

38

RNA structures (DSSR) / Re: plotting the helical axis along curved helices

« Last post by xiangjun on October 25, 2024, 08:46:14 pm »

Hi Di,

Do you have any idea of how to easily find the axis of each 2-bp segment of a helix?

The info is within DSSR, but not exposed. I'm considering to add this feature in DSSR JSON output for easy parsing. For WC-like pairs, things are not that complicated. However, with there are subtitles with non-Watson-Crick pairs, e.g., Hoogsteen and reverse Hoogsteen base pairs.

Also, I think an easier solution for A-form helix is to do a shift of the origin in the plane of the reference frame so that the shifted origin is where the axis passes through the plane.

See "Worked examples on base-pair parameters" in the DSSR Pro User Manual. especially Session "6 Local helical parameters". The vectors o1_h and o2_h are what you need. They are not simple shifts of the origin in the reference frame.

This thread actually prompt me to refine the detailed algorithmic descritpion and get the content published. They are the real meat of 3DNA!

Best regards,

Xiang-Jun

39

RNA structures (DSSR) / Re: plotting the helical axis along curved helices

« Last post by Di_Liu on October 25, 2024, 07:42:23 pm »

Thanks, Xiang-Jun!

Do you have any idea of how to easily find the axis of each 2-bp segment of a helix?

Also, I think an easier solution for A-form helix is to do a shift of the origin in the plane of the reference frame so that the shifted origin is where the axis passes through the plane.

Di

40

RNA structures (DSSR) / Re: plotting the helical axis along curved helices

« Last post by xiangjun on October 24, 2024, 10:53:08 pm »

Hi Di,

Thanks for posting on the Forum. Indeed the origins of base-pairs are centered within a pair, as defined in the standard base reference frame. For B-form DNA where the helical axis passes through and is perpendicular to base pairs, the line connecting bp origins appears as expected. For A-form DNA or RNA (which is in A-form), the helical axis passes through the central hole where the bps (and their origins) spiral around. See "Figure 4. Influence of non‐zero Slide and Roll at sequential dimer steps on overall DNA helical conformation" of the 2003 3DNA paper in NAR.

DSSR does output a linear helical axis when a helical segment is not too strongly curved. See the 2015 DSSR paper "Figure 2 -- analysis of the yeast phenylalanine tRNA (1ehz)" for an example. You could also run the following commands:

Code: [Select]

x3dna-dssr -i=1ehz.pdb --helical-axis
pymol 1ehz.pdb dssr-helicalAxes.pdb
# within PyMOL: as lines; png 1ehz-helices.png
You will see an image as attached below.

However, DSSR currently does not fit a smooth curvilinear helical axis around an arbitrary shape, e.g., a DNA circle. In principle, DSSR can fit a mini-helical axis for each base-pair step (i.e., a 2-bp segment) and then perform a b-spline interpolation. I'm open to suggestions and welcome collaborations to pursue this topic further.

Best regards,

Xiang-Jun