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Recently I've read Dr. Lu's paper "The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex (http://nar.oxfordjournals.org/content/38/14/4868.full)".
I found that Fig1.C
(https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/nar/38/14/10.1093_nar_gkq155/1/gkq155f1.jpeg?Expires=1576905455&Signature=Dl65sXAdNDgPJmeaXg2XS~96C98WAGiRWN530KhjTFdodEz7WpbGZlaggZIfpbMC1Nzfd6eDQMxFICDYt~HieKC3Hg00r2X~zb6rNaJVTtfwXYKQm4Ubww0I3Q0CBjs89Mc4d-ohGUkFqP-wX3Hi-FBn-UBNOcfIGASKICUlmLCoFMKJPS5IEqmgO8NLX2MdizfSdo0ZkjF2LC~SkmvuzLnnF3p-h8y2d4LinOV9j1EMdAP4MFTn8RRrS6IReZQfZoT5dJe4o3B6dHvKocIRChfHGH2lhp43UFzCqiGfSQ-xbMHpJzDW6y~juXFpw4AEZ5juPj1wtsbeUnI01K-wYQ__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA)
in the paper above is a very nice representation for plotting the histogram of angle. Dr. Lu, could share your experience with this plot with us? Thank you!
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Thanks for your interest in my GpU paper. I am glad that your find Fig 1C "a very nice representation for plotting the histogram of angle".
Per your request, here is the detailed step-by-step procedure I originally used to generate Fig 1C, up to the "raw" histogram of the phase angle of sugar ring pseudorotation.
- The data file named "key_pars_gu193.txt" is attached. It contains the phase angle of pseudorotation of the U and G sugar rings.
- The following R script is used to generate the "raw" figure (attached).
library("circular")
pdat <- read.delim("key_pars_gu193.txt")
attach(pdat)
xfig(file="sugar_raw.fig", onefile=TRUE)
par(mfrow = c(1,2))
plot(circular(p1, units="degrees", rotation="clock"), zero=pi/2,
stack=TRUE, bins=150, shrink=1.5)
plot(circular(p2, units="degrees", rotation="clock"), zero=pi/2,
stack=TRUE, bins=150, shrink=1.5)
par(mfrow = c(1,1))
dev.off()
Please note the followings:- The R 'circular' package is used (http://cran.r-project.org/web/packages/ ... index.html (http://cran.r-project.org/web/packages/circular/index.html))
- The xfig (http://www.xfig.org/ (http://www.xfig.org/)) output device is used for later manually editing (not data points, but only cosmetic styles, of course) of the generated figure.
[attachment=1:1vq0n9no]key_pars_gu193.txt[/attachment:1vq0n9no]
[attachment=0:1vq0n9no]sugar_raw.png[/attachment:1vq0n9no]
HTH,
Xiang-Jun
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
