R: Deformation Analysis

deformation.nma {bio3d} | R Documentation

## Deformation Analysis

### Description

Calculate deformation energies from Normal Mode Analysis.

### Usage

    deformation.nma(nma, mode.inds = NULL, pfc.fun = NULL, ncore = NULL)

### Arguments

`nma` | a list object of class `"nma"` (obtained with `nma`).
`mode.inds` | a numeric vector of mode indices in which the calculation should be based.
`pfc.fun` | customized pair force constant (‘pfc’) function. The provided function should take a vector of distances as an argument to return a vector of force constants. See `nma` for examples.
`ncore` | number of CPU cores used to do the calculation. `ncore>1` requires package ‘parallel’ installed.

### Details

Deformation analysis provides a measure for the amount of local flexibility of the protein structure - i.e. atomic motion relative to neighbouring atoms. It differs from ‘fluctuations’ (e.g. RMSF values) which provide amplitudes of the absolute atomic motion.

Deformation energies are calculated based on the `nma` object. By default the first 20 non-trivial modes are included in the calculation.

See examples for more details.

### Value

Returns a list with the following components:

`ei` | numeric matrix containing the energy contribution (E) from each atom (i; row-wise) at each mode index (column-wise).
`sums` | deformation energies corresponding to each mode.

### Author(s)

Lars Skjaerven

### References

Hinsen, K. (1998) Proteins 33, 417–429. Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

### See Also

`nma`

### Examples

    # Running the example takes some time - testing excluded

    ## Fetch stucture
    pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )

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

    ## Calculate deformation energies
    def.energies <- deformation.nma(modes)

    ## Not run:
    ## Fluctuations of first non-trivial mode
    def.energies <- deformation.nma(modes, mode.inds=seq(7, 16))

    write.pdb(pdb=NULL, xyz=modes$xyz,
              b=def.energies$ei[,1])

    ## End(Not run)

[Package bio3d version 2.3-3 Index]