How to visualise the secondary structure of pc1.pdb?

[Cheng]

p1 <- mktrj.pca(pc, pc=1, b=pc$au[,1], file="pc1.pdb") outputs a pdb based on Principal Component 1, but with only alpha-carbon atoms in the pc1.pdb file (This link)

It looks like this in Pymol:

In VMD, only dots are presented:

So can I view the whole structure of it, so that secondary structure can be seen? I think this requires the pc1.pdb file containing full atoms. Is this doable?

Thank you.

Yours sincerely

Cheng

[Barry Grant]

IN VMD you can use the tube representation to see the trace of CA atoms.

If you want to see secondary structure type interactions you will want to include backbone atoms in your analysis and then you can write those out with the mktrj like functions also.

[Cheng]

Thank you so much! The tube representation could show the connection!

For "include backbone atoms", I tried this:

dcd <- read.dcd(dcdfile)
pdb <- read.pdb(pdbfile)
bb.inds <- atom.select(pdb, "backbone")
xyz <- fit.xyz(fixed=pdb$xyz, mobile=dcd, fixed.inds=bb.inds$xyz, mobile.inds=bb.inds$xyz)
pc <- pca.xyz(xyz[,bb.inds$xyz])
p1 <- mktrj.pca(pc, pc=1, b=pc$au[,1], file="pc1_bb.pdb")

But I got this file with all the atoms as alanines. So did I do it correctly?

[Barry Grant]

You can set the atom and residue names to match your case.

bb.pdb <- trim.pdb(pdb, "back")
mktrj.pca(pc, pc=1, pdb=bb.pdb, file="pc1_bb.pdb")