Web 3DNA is highlighted in the cover image

[xiangjun]

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, and the lower-left image is as Fig. 2A. The lower-right image is sort of like Fig. 1D. However, it was actually generated using DSSR and PyMOL with (long) base-pair blocks for Watson-Crick pairs, with the 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:

• 1fir-rebuild.pdb -- a tRNA model generated with web 3DNA 2.0
• 1fir-raw.pml -- the PyMOL script crated with DSSR (line #1 above)
• 1fir-dssr.pml -- manually edited PyMOL script based on 1fir-raw.pml
• 1fir-dssr.png -- the schematic block images used in the cover image