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Questions and answers => RNA structures (DSSR) => DSSR-Jmol integration => Topic started by: xiangjun on June 30, 2017, 01:56:36 pm

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Title: cover image
Post by: xiangjun on June 30, 2017, 01:56:36 pm
(http://jmol.x3dna.org/cover-image/NAR17-web-cover.png)

Caption: 3D interactive visualization of selected RNA structural features enabled by the DSSR-Jmol integration (http://jmol.x3dna.org (http://jmol.x3dna.org)). Clockwise from upper left: Structure of the xpt-pbuX guanine riboswitch in complex with hypoxanthine (PDB id: 4fe5) in ‘base blocks’ representation. The three-way junction loop encompassing the metabolite (in space-filling representation) is color-coded by base identity: A, red; C, yellow; G, green; U, cyan. The loop-loop interaction (a kissing-loop motif) at the top is highlighted in red (upper left corner). Structure of the Thermus thermophilus 30S ribosomal subunit in complex with antibiotics (PDB id: 1fjg) in step diagram. The 16S ribosomal RNA is color-coded in spectrum with the 5′-end in blue and the 3′-end in red (upper middle). Structure of the classic L-shaped yeast phenylalanine tRNA (PDB id: 1ehz) in step diagram, with the three hairpin loops highlighted in red and the [2,1,5,0] four-way junction loop in blue (upper right corner). Structure of the Pistol self-cleaving ribozyme (PDB id: 5ktj), showcasing (in red) the horizontal helix in space-filling representation. The helix is composed of six short stems stabilized via coaxial stacking interactions (bottom).


Upper left corner (Jmol script: 4fe5.scr (http://jmol.x3dna.org/cover-image/4fe5.scr); image: 4fe5.png (http://jmol.x3dna.org/cover-image/4fe5.png)):
Code: [Select]
# Jmol 14.17.1 (2017-05-27)
load =4fe5/dssr
select nts; display nts
rotate best; rotate z 90; rotate y 50
cartoon only
set cartoonsteps off
set cartoonblocks on
set antialiasdisplay on
background white; color grey
select within(dssr, "junctions..1"); color nucleic
select within(dssr, "junctions..2"); color red
select HPA; cpk; color cpk
frank off
write PNGJ 3000 3000 4fe5-raw.png


Upper middle (Jmol script: 1fjg.scr (http://jmol.x3dna.org/cover-image/1fjg.scr); image: 1fjg.png (http://jmol.x3dna.org/cover-image/1fjg.png)):
Code: [Select]
# Jmol 14.17.1 (2017-05-27)
load =1fjg/dssr
select nts; display nts
rotate best; rotate z 90
cartoon only
set cartoonsteps on
set cartoonblocks off
set antialiasdisplay on
background white; color monomer
frank off
write PNGJ 3000 3000 1fjg-raw.png


Upper right corner (Jmol script: 1ehz.scr (http://jmol.x3dna.org/cover-image/1ehz.scr); image: 1ehz.png (http://jmol.x3dna.org/cover-image/1ehz.png)):
Code: [Select]
# Jmol 14.17.1 (2017-05-27)
load =1ehz/dssr
select nts; display nts
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
frank off
write PNGJ 3000 3000 1ehz-raw.png


Bottom (Jmol script: 5ktj.scr (http://jmol.x3dna.org/cover-image/5ktj.scr); image: 5ktj.png (http://jmol.x3dna.org/cover-image/5ktj.png)):
Code: [Select]
# Jmol 14.17.1 (2017-05-27)
load =5ktj/dssr
select nts; display nts
rotate best
cartoon only
set cartoonsteps off
set cartoonblocks off
set antialiasdisplay on
background white; color grey
select within(dssr, "helices..2"); color red; cpk
frank off
write PNGJ 3000 3000 5ktj-raw.png



The 'raw' images were automatically generated from the corresponding script files via command line using the Jmol application with options -ions. The ImageMagick convert program was used to remove empty boundaries. Using 4fe5 as an example, the procedure is as follows:

Code: [Select]
jmol -ions 4fe5.scr   # generate 4fe5-raw.png
convert -trim +repage -border 10 -bordercolor white 4fe5-raw.png 4fe5.png

The four images were then combined using InkScape (https://inkscape.org/en/), and exported to one big composite PNG file (DSSR-Jmol-for-NAR17-web-cover.png (http://jmol.x3dna.org/cover-image/DSSR-Jmol-for-NAR17-web-cover.png), 18MB).


Finally, the tarball file, reproduce-dssr-jmol.tar.gz (http://jmol.x3dna.org/reproduce/reproduce-dssr-jmol.tar.gz), contains all the scripts and data files for reproducing the cover image.

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.