library(ncdf)
library(bio3d)
load(file="xrayPCA_EQ.RData")

pdb.closed <- read.pdb("1XCK_chainA_noWAT_noH.pdb")
##inds <- atom.select(pdb, "///500:515///CA/")
ca.inds <- atom.select(pdb.closed, "calpha")


e1 <- gaps.pos$f.inds[atom2xyz(1:134)] ## from Ala3
e2 <- gaps.pos$f.inds[atom2xyz(408:522)] ## to Leu524
eq <- c(e1,e2)

e1 <- atom2xyz(2:135)
e2 <- atom2xyz(409:523)
eq.md <- c(e1,e2)




trj.inds <- seq(1001, 2000, by=1)
sim171 <- NULL
prefix171 <- "/net/lutefisk/slars/groel_md/1XCK_rhodanese/171_1XCK_rhodanese_ATP/results/traj_monomer/"

prefix <- "20-50ns_noWAT_1500frames_noATP_noH_chain_"
#prefix <- "100ns_noWAT_2000frames_noATP_noH_chain_"
#
for ( i in 1:7 ) {
  tmptrj <- read.ncdf(paste(prefix171, prefix, i , ".nc", sep=""))
  sim171$xyzfit[[i]] <- fit.xyz(fixed = pdbs$xyz[1, ],
                                mobile = tmptrj[trj.inds, ca.inds$xyz],
                                fixed.inds = core$c1A.xyz,
                                mobile.inds = core$c1A.xyz,
                                full.pdbs = FALSE)
}


for ( i in 8:14 ) {
  tmptrj <- read.ncdf(paste(prefix171, prefix, i , ".nc", sep=""))
  sim171$xyzfit[[i]] <- fit.xyz(fixed = pdbs$xyz[1,gaps.pos$f.inds],
                                mobile = tmptrj[trj.inds, ca.inds$xyz],
                                fixed.inds = core$c1A.xyz,
                                mobile.inds = core$c1A.xyz,
                                full.pdbs = FALSE)
}






tmptrj <- NULL
for ( i in 1:7 ) {
  tmptrj=rbind(tmptrj, sim171$xyzfit[[i]])
}
sim171$cis$proj <- pca.project(tmptrj[,eq.md], pc.xray)


tmptrj <- NULL
for ( i in 8:14 ) {
  tmptrj=rbind(tmptrj, sim171$xyzfit[[i]])
}
sim171$trans$proj <- pca.project(tmptrj[,eq.md], pc.xray)

sim171$xyzfit <- NULL


save(sim171, file="projected_GroEL_rhod_last50ns.RData")