PCA: How to project the holo trajectory onto the first two eigenvectors of the apo one

[Former user]

Hi, I would like to preform PCA for the holo and apo forms of a protein. To detect differences between both forms I would like to project the holo trajectory onto a subset, i.e., the first two, eigenvectors of the apo trajectory. Can I do that using Bio3d? Kind regards, Jorge

[Lars Skjærven]

Absolutely. Make sure you superimpose both trajectories to the same structure. Then use pca.xyz() to calculate the PCs of apo. Project the holo traj onto apo-PCs with project.pca(). Plot with plot.pca().

# read in calpha trajectories
apo <- read.ncdf("apo.nc")
holo <- read.ncdf("holo.nc")

# superimpose (same number of calpha atoms)
xyz1 <- fit.xyz(apo[1, ], apo)
xyz2 <- fit.xyz(apo[1, ], holo)

# perform PCA
pc <- pca.xyz(xyz1)

# project holo traj to PCs
proj2 <- project.pca(xyz2, pc)

# blues for apo
cols1 <- densCols(pc$z[,1:2])

# yellow-orange for holo
cr <-  colorRampPalette(c("#FCFF00", "#FF9400", "#FF3100"))
cols2 <- densCols(proj2[,1:2], colramp=cr)

# plot projections
plot(pc$z[, 1:2], col=cols1, pch=16)
points(proj2[, 1:2], col=cols2, pch=16)