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###
### Examples from NMA Vignette
###
### Authors Lars Skjaerven
### Xin-Qiu Yao
### Barry J Grant
###
require(bio3d); require(graphics);
pause <- function() {
cat("Press ENTER/RETURN/NEWLINE to continue.")
readLines(n=1)
invisible()
}
#############################################
## #
## Basic usage #
## #
#############################################
### Read PDB and Calculate Normal Modes
pdb <- read.pdb("1hel")
modes <- nma(pdb)
pause()
### Print a summary
print(modes)
pause()
### Plot the nma object for a quick overview
plot(modes)
pause()
### Calculate cross-correlations
cm <- dccm(modes)
pause()
### Plot correlation map
plot(cm, sse=pdb)
pause()
### Calculate modes with force field ANM
modes.anm <- nma(pdb, ff="anm")
pause()
### Investigate modes similarity with RMSIP
r <- rmsip(modes, modes.anm)
pause()
### Plot RMSIP results
plot(r, xlab="ANM", ylab="C-alpha FF")
pause()
################################################
## #
## Ensemble NMA #
## (requires the 'muscle' program installed) #
## #
################################################
pause()
### Set temp dir to store PDB files
tmp.dir <- tempdir()
### Download a set of DHFR structures
ids <- c("1rx2_A", "1rx4_A", "1rg7_A",
"3fyv_X", "3sgy_B")
### Download and split by chain ID
raw.files <- get.pdb(ids, path=tmp.dir)
pause()
### Split PDB files by chain ID
files <- pdbsplit( raw.files, ids, path=tmp.dir)
pause()
### Align structures
pdbs <- pdbaln(files)
pause()
### View sequence identity
summary( c(seqidentity(pdbs)) )
pause()
### Calculate modes of aligned proteins
modes <- nma(pdbs)
pause()
## Print a summary
print(modes)
pause()
### Plot fluctuations
plot(modes, pdbs)
pause()
### Cluster Modes simiarlity
heatmap(1-modes$rmsip, labCol=ids)
unlink(tmp.dir)
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