R and bio3d : Dynamic Cross-Correlation from Normal Modes Analysis

ccm.R

# if bio3d not installed uncomment this
# install.packages('bio3d')

library('bio3d')

## Fetch stucture from RCSB
pdb <- read.pdb("1hel")
# or from local file
# pdb <- read.pdb('my.pdb')

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## Dynamic Cross-Correlation from Normal Modes Analysis

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

## Calculate correlation matrix
cm <- dccm.nma(modes)

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

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