dccm.gnm.Rd
Calculate the crosscorrelation matrix from Gaussian network model normal modes analysis.
# S3 method for gnm dccm(x, ...) # S3 method for egnm dccm(x, ...)
x  an object of class ‘gnm’ or ‘egnm’ as obtained from


...  additional arguments (currently ignored). 
Returns a crosscorrelation matrix.
This function calculates the crosscorrelation matrix from Gaussian network
model (GNM) normal modes analysis (NMA) obtained from gnm
. It returns
a matrix of residuewise crosscorrelations whose elements, Cij, may be
displayed in a graphical representation frequently termed a dynamical
crosscorrelation map, or DCCM. (See more details in help(dccm.nma)
).
XinQiu Yao & Lars Skjaerven
Bahar, I. et al. (1997) Folding Des. 2, 173.
## 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))