ind.adj <- atom.select(pdb,elety=“CA”,re sno=1:505)

trj.fit.adj <- fit.xyz(pdb$xyz[ind.adj$xyz], dcd[,ind.adj$xyz])

trj.pca.adj <- pca.xyz(trj.fit.adj)

rf.adj <- rmsf(trj.fit.adj)

barplot(rf.adj,col=“purple”,border=“purple”,main=“Adjusted”)

par(new=TRUE)

plot(trj.pca.adj$au[,1],type=“l”,col=“orange”,lwd=3)

points(trj.pca.adj$au[,2],type=“l”,col=“green”,lwd=3)

points(trj.pca.adj$au[,3],type=“l”,col=“sky blue”,lwd=3)