RMSF figure similar to Biophysical Journal Vol 107 Nov. 2014 pp 2204-2213

[Former user]

Greetings,

I am wondering if and how I can make a figure similar to figure 1 of the above mentioned paper without having to compute the rmsf with bio3d. For instance, I have collected the RMSF measurements using another program and I would like to just make the figure with R/bio3d. Is this possible?

[Lars Skjærven]

Absolutely. The rmsf() function in bio3d returns a numeric vector which is subsequently used for plotting with functions like plotb3() or just plot(). If you have rmsf e.g. from cpptraj, use read.table() to read the rmsf values.

[debra ragland]

Hi, yes I've figured out how to plot rmsf values calculated elsewhere using the plotb3 function, however, I am moreso wondering about the annotations in figure 1 of the aforementioned paper. Are these a feature of bio3d or were they added in another program? Annotations meaning the labels and blue reactangles, I have managed to add the sse elements using the plotb3 function as well.

[Lars Skjærven]

You can explore function plot.fluct() which has the functionality of checking for significant differences between groups of fluctuation profiles. Input to plot.fluct is a matrix of RMSF values in which the individual structures are stored row-wise. See help(plot.fluct) for more information.

Note that these rectangles can be added to any plot in R. Quick example below shows how to combine with plotb3(). Text can be added using function text().

> plot.new()
> plot.window(xlim=xlim, ylim=ylim)

# plot blue rectangles
> rect(25, ylim[1], 35, ylim[2], col="lightblue", border=NA)

# plot fluctuation profile
> par(new=TRUE)
> plotb3(x[1,], sse=sse, resno=resno)

# legend
> legend('topright', legend=label, text.col=col, bty='n')