mktrj.pca() does not write out pdb for project.pca

Hi,

Am been projecting the X-ray structures on the simulation PCA’s. I performed the following commands:

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dcd <- read.dcd('tmp.dcd')
pdb <- read.pdb('tmp.pdb')
ids <- c("6GBR_A","6XOA_A")
raw.files <-get.pdb(ids)
files <- pdbsplit(raw.files, ids)
pdbs <- pdbaln(files)
core <- core.find(pdbs)
pdbs$xyz = pdbfit(pdbs, core$c0.5A.xyz)
gaps.pos <- gap.inspect(pdbs$xyz)
gaps.res <- gap.inspect(pdbs$ali)
pc.xray <- pca.xyz(pdbs$xyz[,gaps.pos$f.inds])
plot(pc.xray)
inds <- pdb2aln.ind(pdbs, pdb, gaps.res$f.inds)
inds.core <- pdb2aln.ind(pdbs, pdb, core$c0.5A.atom)
trj.fit <- fit.xyz(pdbs$xyz[1,], dcd, core$c0.5A.xyz, inds.core$b$xyz)
proj <- project.pca(trj.fit[, inds$b$xyz], pc.xray)
plot(proj[,1:2], xlim=c(-15,15),ylim=c(-15,15),pch=19,typ="p")
points(pc.xray$z[,1:2], col=1, pch=4)

so the proj[,1:2] gives me the PCA for the PC1 and 2 of the projected PC’s. But now to look at the RMSF and write out the mktrj.pca i cant directly give the “proj”. What should be the commands for this?

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