bio3d (version 2.4-4)

dccm.gnm: Dynamic Cross-Correlation from Gaussian Network Model

Description

Calculate the cross-correlation matrix from Gaussian network model normal modes analysis.

Usage

# S3 method for gnm
dccm(x, ...)
# S3 method for egnm
dccm(x, ...)

Value

Returns a cross-correlation matrix.

Arguments

x

an object of class ‘gnm’ or ‘egnm’ as obtained from gnm.

...

additional arguments (currently ignored).

Author

Xin-Qiu Yao & Lars Skjaerven

Details

This function calculates the cross-correlation matrix from Gaussian network model (GNM) normal modes analysis (NMA) obtained from gnm. It returns a matrix of residue-wise cross-correlations whose elements, Cij, may be displayed in a graphical representation frequently termed a dynamical cross-correlation map, or DCCM. (See more details in help(dccm.nma)).

References

Bahar, I. et al. (1997) Folding Des. 2, 173.

See Also

gnm, dccm.nma, dccm.enma, plot.dccm.

Examples

## Fetch stucture
pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )
   
## Calculate normal modes
modes <- gnm(pdb)
   
## Calculate correlation matrix
cm <- dccm(modes)

## Plot correlation map
plot(cm, sse = pdb, contour = FALSE, col.regions = bwr.colors(20),
     at = seq(-1, 1, 0.1))