Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · Reproduce DSSR · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Author Topic: How to make a nice visualization for angle distribution?  (Read 2497 times)

Offline whuang

  • regular
  • *
  • Posts: 1
    • View Profile
How to make a nice visualization for angle distribution?
« on: October 12, 2010, 11:22:56 am »
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".

I found that Fig1.C

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!
« Last Edit: December 14, 2013, 11:33:01 am by xiangjun »

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1215
    • View Profile
    • 3DNA homepage
Re: How to make a nice visualization for angle distribution?
« Reply #1 on: October 12, 2010, 11:30:56 pm »
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).
    Code: [Select]
    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:  
[attachment=1:1vq0n9no]key_pars_gu193.txt[/attachment:1vq0n9no]
[attachment=0:1vq0n9no]sugar_raw.png[/attachment:1vq0n9no]
HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.