Extracting data from bio3d plots

[Former user]

Hi,

I'm very new to bio3d and ask that you please bare with me. I want to know if its possible to extract the data from the bio3d plots so that I can re-plot them with other graphing software? Mostly i just want them to look like the other plots in my publication.

Any help would be much appreciated!

[Lars Skjærven]

Absolutely - you can easily extract the raw data from whatever you have generated in R / bio3d. Typically you call a function for a particular calculation - e.g. function nma(). This will output an object containing all data which is used in plotting - e.g. residue fluctuations. To save this raw data to a file in which you can open elsewhere you can use functions such as write.table:

> pdb <- read.pdb("1hel")
> m <- nma(pdb)
> m$fluctuations
> write.table(m$fluctuations, file="nma_flucts.dat")

[sayman]

Thanks so much! very helpful indeed. Don't know how i could have missed it.