3DNA Forum

Questions and answers => RNA structures (DSSR) => DSSR-Jmol integration => Topic started by: xiangjun on May 04, 2017, 01:35:32 pm

Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Video Overview · DSSR v2.5.0 (DSSR Manual) · Homepage

Title: The graphical abstract
Post by: xiangjun on May 04, 2017, 01:35:32 pm

(http://jmol.x3dna.org/reproduce/dssr-jmol-abstract-graphics-annotated.png)

3D interactive visualization of the classic L-shaped tRNA (PDB id: 1ehz) with the three hairpin loops highlighted in red and the four-way junction loop in blue. The image was created using the DSSR-Jmol integration.

---

The Jmol script (abstract-graphics.scr (http://jmol.x3dna.org/reproduce/abstract-graphics.scr)) used to create the original image is shown below. The image was annotated using Inkscape (https://inkscape.org/en/).

Code: [Select]

# Jmol 14.13.1 (2017-04-09)
load =1ehz/dssr
select nucleic; display nucleic
rotate best; rotate z 90
cartoon only
set cartoonsteps on
set cartoonblocks off
set antialiasdisplay on
background white; color grey
select hairpins; color red
select junctions; color blue

The raw image from the above script is as below:

(http://jmol.x3dna.org/reproduce/dssr-jmol-abstract-graphics.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