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Questions and answers => w3DNA -- web interface to 3DNA => web 3DNA 2.0 (http://web.x3dna.org) => Topic started by: xiangjun on June 28, 2019, 10:59:26 pm

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Title: Web 3DNA is highlighted in the cover image
Post by: xiangjun on June 28, 2019, 10:59:26 pm
(http://docs.x3dna.org/images/w3DNA-v2-cover-image.png)

Caption: Examples of customized molecular models that can be generated with 3DNA: (top) a chromatin-like, nucleosome-decorated DNA with the structures of known histone-DNA assemblies placed at user-defined binding sites; (lower left) molecular schematic of a DNA trinucleotide diphosphate illustrating the base planes and reference frames used to construct and analyze 3D nucleic acid-containing structures; (lower right) customized single-stranded tRNA model built from a user-defined base sequence and a set of rigid-body parameters describing the desired placement of successive bases. Color code of base blocks: A, red; C, yellow; G, green; T, blue; U, cyan.



The top image is as Fig. 1E (http://forum.x3dna.org/w3dna-v2/figure-1-summary-of-web-3dna-2-0/), and the lower-left image is as Fig. 2A (http://forum.x3dna.org/w3dna-v2/figure-2-new-structural-parameters). The lower-right image is sort of like Fig. 1D (http://forum.x3dna.org/w3dna-v2/figure-1-summary-of-web-3dna-2-0/). However, it was actually generated using DSSR (http://forum.x3dna.org/dssr-nar-paper/) and PyMOL with (long) base-pair blocks (https://pymolwiki.org/index.php/Dssr_block) for Watson-Crick pairs, with he commands used listed below:

Code: Bash
  1. x3dna-dssr -i=1fir-rebuild.pdb --blocview --block-opts=wc-minor -o=1fir-raw.pml
  2.  
  3. # Manually re-oriented the block image: "turn z, -155", and
  4. #     changed the chain color from "red" (default for chain A) to "marine"
  5. #     ray-traced and rendered to a PNG image, "1fir-dssr-pymol.png".
  6. # The revised PYMOL .pml file is named "1fir-dssr.pml"
  7. pymol -qkc 1fir-dssr.pml
  8. # The above PyMOL command generates "1fir-dssr-pymol.png", which is trimmed as below
  9. convert -trim +repage -transparent white 1fir-dssr-pymol.png 1fir-dssr.png

The following key related files are attached:

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.