# NOT RUN {
# }
# NOT RUN {
#-- Read transducin alignment and structures
aln <- read.fasta(system.file("examples/transducin.fa",package="bio3d"))
pdbs <- read.fasta.pdb(aln)
# Find core
core <- core.find(pdbs,
#write.pdbs = TRUE,
verbose=TRUE)
rm(list=c("pdbs", "core"))
# }
# NOT RUN {
#-- OR for demo purposes just read previously saved transducin data
attach(transducin)
# Previously fitted coordinates based on sub 1.0A^3 core. See core.find() function.
xyz <- pdbs$xyz
#-- Do PCA ignoring gap containing positions
pc.xray <- pca.xyz(xyz, rm.gaps=TRUE)
# Plot results (conformer plots & scree plot overview)
plot(pc.xray, col=annotation[, "color"])
# Plot a single conformer plot of PC1 v PC2
plot(pc.xray, pc.axes=1:2, col=annotation[, "color"])
## Plot atom wise loadings
plot.bio3d(pc.xray$au[,1], ylab="PC1 (A)")
# }
# NOT RUN {
# PDB server connection required - testing excluded
## Plot loadings in relation to reference structure 1TAG
pdb <- read.pdb("1tag")
ind <- grep("1TAG", pdbs$id) ## location in alignment
resno <- pdbs$resno[ind, !is.gap(pdbs)] ## non-gap residues
tpdb <- trim.pdb(pdb, resno=resno)
op <- par(no.readonly=TRUE)
par(mfrow = c(3, 1), cex = 0.6, mar = c(3, 4, 1, 1))
plot.bio3d(pc.xray$au[,1], resno, ylab="PC1 (A)", sse=tpdb)
plot.bio3d(pc.xray$au[,2], resno, ylab="PC2 (A)", sse=tpdb)
plot.bio3d(pc.xray$au[,3], resno, ylab="PC3 (A)", sse=tpdb)
par(op)
# }
# NOT RUN {
# }
# NOT RUN {
# Write PC trajectory
resno = pdbs$resno[1, !is.gap(pdbs)]
resid = aa123(pdbs$ali[1, !is.gap(pdbs)])
a <- mktrj.pca(pc.xray, pc=1, file="pc1.pdb",
resno=resno, resid=resid )
b <- mktrj.pca(pc.xray, pc=2, file="pc2.pdb",
resno=resno, resid=resid )
c <- mktrj.pca(pc.xray, pc=3, file="pc3.pdb",
resno=resno, resid=resid )
# }
# NOT RUN {
detach(transducin)
# }
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