"dccm"(x, nmodes = NULL, ncore = NULL, ...)
nma as obtained from
function nma. ncore>1 requires package ‘parallel’ installed. Calculate the cross-correlation matrix from Normal Modes Analysis.
This function calculates the cross-correlation matrix from Normal
Modes Analysis (NMA) obtained from nma of a protein
structure. 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.
If Cij = 1 the fluctuations of residues i and j are completely correlated (same period and same phase), if Cij = -1 the fluctuations of residues i and j are completely anticorrelated (same period and opposite phase), and if Cij = 0 the fluctuations of i and j are not correlated.
Wynsberghe. A.W.V, Cui, Q. Structure 14, 1647--1653. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
## Fetch stucture pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") ) ## Calculate normal modes modes <- nma(pdb)Building Hessian... Done in 0.047 seconds. Diagonalizing Hessian... Done in 0.139 seconds.## Calculate correlation matrix cm <- dccm.nma(modes)|======================================================================| 100%## Plot correlation map plot(cm, sse = pdb, contour = FALSE, col.regions = bwr.colors(20), at = seq(-1, 1, 0.1))