bio3d (version 2.1-1)

fluct.nma: NMA Fluctuations

Description

Calculates the atomic fluctuations from normal modes analysis.

Usage

fluct.nma(nma, mode.inds=NULL)

Arguments

nma

a list object of class "nma" (obtained with nma).

mode.inds

a numeric vector containing the the mode numbers in which the calculation should be based.

Value

• Returns a numeric vector of atomic fluctuations.

Details

Atomic fluctuations are calculated based on the nma object. By default all modes are included in the calculation.

See examples for more details.

References

Hinsen, K. et al. (2000) Chemical Physics 261, 25--37. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

See Also

nma

Examples

## Fetch stucture
pdb <- read.pdb("1hel")

## Calculate (vibrational) normal modes
modes <- nma(pdb)

## Fluctuations
f <- fluct.nma(modes)

## Fluctuations of first non-trivial mode
f <- fluct.nma(modes, mode.inds=c(7,8))