PCA for crystal structure and MD simulation

[Aiswarya Pawar]

Hi All,

I’am successfully able to plot PCA for set of crystal structures and the trajectories separately. But i want to plot them together, basically something like projecting one over other. Below i have mentioned individual pca scripts.

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for crystal structure-

ids <- c("4LDJ_A","5VQ6_A","5VQ8_A","4L8G","4LPK")
raw.files <-get.pdb(ids)
files <- pdbsplit(raw.files, ids)
pdbs <- pdbaln(files)

pc <- pca(pdbs, rm.gaps=TRUE)
plot(pc,pc.axes=1:2)

for MD trajectory

dcd <- read.dcd('trj.dcd')

pdb <- read.pdb('trj.pdb')

ca.inds <- atom.select(pdb, elety = 'CA')

xyz <- fit.xyz(fixed=pdb$xyz,mobile=dcd, fixed.inds=ca.inds$xyz,mobile.inds=ca.inds$xyz)

pc <- pca.xyz(xyz[, ca.inds$xyz])

plot(pc, col=bwr.colors(nrow(xyz)))

[Aiswarya Pawar]

Please can anyone help with this query!

[Xinqiu Yao]

Hi,

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What you need is just the project.pca() function to project crystal structures onto MD PCs or vice versa (see ?project.pca for more detail.

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After the projection, you can add extra data points by e.g. points() or make a new plot with trajectory and crystal structures together.