Nothing
###
### Example of PCA on a collection of PKA structures
### and a large collection of transducin structure
###
### Authors Xin-Qiu Yao
### Lars Skjaerven
### Barry J Grant
###
require(bio3d); require(graphics);
pause <- function() {
cat("Press ENTER/RETURN/NEWLINE to continue.")
readLines(n=1)
invisible()
}
################################################
## #
## Basic PCA of related X-ray structures #
## (requires the 'muscle' program installed) #
## #
################################################
pause()
### Set temp dir to store PDB files
tmp.dir <- tempdir()
## Specify PDB identifiers
ids <- c("1cdk_A", "3agm_A", "1cmk_E",
"3dnd_A", "1q8w_A")
## Download PDBs
raw.files <- get.pdb(ids, path=tmp.dir)
pause()
## Split PDBs by chain ID
files <- pdbsplit(raw.files, ids, path=tmp.dir)
pause()
## Sequence/structure alignment
pdbs <- pdbaln(files)
pause()
## Find invariant core
core <- core.find(pdbs)
pause()
## Fit structures to core region
xyz <- pdbfit(pdbs, inds=core$c1A.xyz)
## outpath="core_fit/", full.pdbs=T, het2atom=T)
pause()
## Locate gap containing positions
gaps.pos <- gap.inspect(pdbs$xyz)
## Perform PCA on non-gap containing positions
pc.xray <- pca.xyz(xyz[,gaps.pos$f.inds])
pause()
## Plot x-ray results
plot(pc.xray)
pause()
#############################################
## #
## Larger transducin example #
## #
#############################################
data(transducin)
attach(transducin, warn.conflicts=FALSE)
## data 'transducin' contains objects
## - pdbs: aligned C-alpha coordinates for 53 transducin
## structures from the PDB
## - annotation: annotation of the 53 PDBs
## Note that this data can be generated from scratch by following the
## Comparative Structure Analysis with Bio3D Vignette available both
## on-line and from within the Bio3D package.
pdbs <- transducin$pdbs
annotation <- transducin$annotation
pause()
## Inspect gaps
gaps.pos <- gap.inspect(pdbs$xyz)
## Previously fitted coordinates invariance core
xyz <- pdbs$xyz
## Do PCA
pc.xray <- pca.xyz(xyz[, gaps.pos$f.inds])
pause()
## Plot overview
plot(pc.xray, col=annotation[, "color"])
## Plot atom wise loadings
plot.bio3d(pc.xray$au[,1], ylab="PC1 (A)")
pause()
unlink(tmp.dir)
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