Calculates the atomic fluctuations from normal modes analysis.
a list object of class
a numeric vector containing the the mode numbers in which the calculation should be based.
Atomic fluctuations are calculated based on the
nma object. By
default all modes are included in the calculation.
See examples for more details.
Returns a numeric vector of atomic fluctuations.
Hinsen, K. et al. (2000) Chemical Physics 261, 25--37. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
## Fetch stucture pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") ) ## Calculate (vibrational) normal modes modes <- nma(pdb)#> Building Hessian... Done in 0.01 seconds. #> Diagonalizing Hessian... Done in 0.078 seconds.## Fluctuations f <- fluct.nma(modes) ## Fluctuations of first non-trivial mode f <- fluct.nma(modes, mode.inds=c(7,8))