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Title: DSSR-PyMOL enabled schematics on the covers of the RNA Journal
Post by: xiangjun on December 16, 2024, 04:11:24 pm
Quote
Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org (http://skmatics.x3dna.org)). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74 (https://doi.org/10.1093/nar/gkaa426)).

See the 2020 paper titled "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL (https://doi.org/10.1093/nar/gkaa426)" in Nucleic Acids Research and the corresponding Supplemental PDF (http://skmatics.x3dna.org/gkaa426-supp.pdf) for details. Many thanks to Drs. Wilma Olson and Cathy Lawson for their help in the preparation of the illustrations.


February 2025 (https://rnajournal.cshlp.org/content/31/2.cover-expansion) (link to the source)

(https://rnajournal.cshlp.org/content/31/2/F1.medium.gif)Structure of the Hendra henipavirus (HeV) nucleoprotein (N) protein-RNA double-ring assembly (PDB id: 8C4H (https://nakb.org/atlas=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 (https://pubmed.ncbi.nlm.nih.gov/38890308/)). 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 (http://skmatics.x3dna.org)). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74 (https://doi.org/10.1093/nar/gkaa426)).


January 2025 (https://rnajournal.cshlp.org/content/31/1.cover-expansion) (link to the source)

(https://rnajournal.cshlp.org/content/31/1/F1.medium.gif)Structure of the helicase and C-terminal domains of Dicer-related helicase-1 (DRH-1) bound to dsRNA (PDB id: 8T5S (https://nakb.org/atlas=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 (https://pubmed.ncbi.nlm.nih.gov/38747717/)). 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 (http://skmatics.x3dna.org)). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74 (https://doi.org/10.1093/nar/gkaa426)).

How are the detailed steps used to generate the above cover image, using DSSR v2.4.6-2024nov15 (http://innovation.columbia.edu/technologies/CU20391):
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 (http://skmatics.x3dna.org/pdb/8t5s/index.html). Whenever feasible, I've integrated features into DSSR to automate routine tasks as much as possible.

Here are the related files:

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

Quote
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).

(http://docs.x3dna.org/images/RNAcovers.png)

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