why different values for fluct.nma(modes, mod.inds=c(7,total.no.of.modes)) and modes$fluctuations?

[Yazhini arangas]

I wanted to get RMSF per residue from nma analysis. If I compare output of fluct.nma(modes) and modes$fluctuations, the values are different. Why is it so? Usually modes$fluctuation gives higher fluctuation than fluct.nma(modes) even though all nma modes are included in the analysis.

a <- read.pdb('BC_pair_wo.pdb')
modes <- nma(a)
modes$fluctuations
fluct.nma(nma =modes, mode.inds = c(7,585))`

Herein, pdb input file and commands output are attached.

[Xinqiu Yao]

Hi,

You should use mode.inds=c(7:585). Note the difference between with and without ':'.

[Lars Skjærven]

Yes, use all non-trivial modes

> p = read.pdb("1hel")
> m = nma(p)
> identical(m$fluctuations, fluct.nma(m))
TRUE