hl.ind <-  c(grep("1XCK_A", id), grep("1SX4_A", id),
             grep("1SX3_A", id), grep("1SX4_N", id) )
hl.col <- c("orange", "green", "red", "yellow")


at.offset=3
mtext.cex=0.75
line=.4
xlim=c(-60,120)
ylim=c(-50,60)
pdf("confplots_noMutants.pdf", w=14, h=4)
par(mfcol=c(2,7), mar=c(3,3,1.5,1), mgp=c(2,1,0))

conf.plot( sim171$cis$proj, pc.xray, mtext="", xlim=xlim, ylim=ylim,
            hl.ind=hl.ind, hl.col=hl.col)
  abline(v=mean(sim129$cis$proj[,1]), lty=2, col="grey60")
  abline(h=mean(sim129$cis$proj[,2]), lty=2, col="grey60")
mtext("(A) WT-ATP (cis)", side=3, line=line, cex=mtext.cex, at=xlim[1]-at.offset, adj=0)

conf.plot( sim171$trans$proj, pc.xray, mtext="", xlim=xlim, ylim=ylim,
            hl.ind=hl.ind, hl.col=hl.col)
  abline(v=mean(sim129$trans$proj[,1]), lty=2, col="grey60")
  abline(h=mean(sim129$trans$proj[,2]), lty=2, col="grey60")
mtext("(B) WT-ATP (trans)", side=3, line=line, cex=mtext.cex, at=xlim[1]-at.offset, adj=0)


conf.plot( sim129$cis$proj, pc.xray, mtext="", xlim=xlim, ylim=ylim,
            hl.ind=hl.ind, hl.col=hl.col)
  abline(v=mean(sim129$cis$proj[,1]), lty=2, col="grey60")
  abline(h=mean(sim129$cis$proj[,2]), lty=2, col="grey60")
mtext("(A) WT-ATP (cis)", side=3, line=line, cex=mtext.cex, at=xlim[1]-at.offset, adj=0)

conf.plot( sim129$trans$proj, pc.xray, mtext="", xlim=xlim, ylim=ylim,
            hl.ind=hl.ind, hl.col=hl.col)
  abline(v=mean(sim129$trans$proj[,1]), lty=2, col="grey60")
  abline(h=mean(sim129$trans$proj[,2]), lty=2, col="grey60")
mtext("(B) WT-ATP (trans)", side=3, line=line, cex=mtext.cex, at=xlim[1]-at.offset, adj=0)

conf.plot( sim116$cis$proj, pc.xray, mtext="", xlim=xlim, ylim=ylim,
            hl.ind=hl.ind, hl.col=hl.col)
  abline(v=mean(sim116$cis$proj[,1]), lty=2, col="grey60")
  abline(h=mean(sim116$cis$proj[,2]), lty=2, col="grey60")
mtext("(C) WT-APO (cis)", side=3, line=line, cex=mtext.cex, at=xlim[1]-at.offset, adj=0)

conf.plot( sim116$trans$proj, pc.xray, mtext="", xlim=xlim, ylim=ylim,
            hl.ind=hl.ind, hl.col=hl.col)
  abline(v=mean(sim116$trans$proj[,1]), lty=2, col="grey60")
  abline(h=mean(sim116$trans$proj[,2]), lty=2, col="grey60")
 mtext("(D) WT-APO (trans)", side=3, line=line, cex=mtext.cex, at=xlim[1]-at.offset, adj=0)



conf.plot( sim162$cis$proj, pc.xray, mtext="", xlim=xlim, ylim=ylim,
            hl.ind=hl.ind, hl.col=hl.col)
  abline(v=mean(sim162$cis$proj[,1]), lty=2, col="grey60")
  abline(h=mean(sim162$cis$proj[,2]), lty=2, col="grey60")
mtext("(E) E434K-ATP (cis)", side=3, line=line, cex=mtext.cex, at=xlim[1]-at.offset, adj=0)

conf.plot( sim162$trans$proj, pc.xray, mtext="", xlim=xlim, ylim=ylim,
            hl.ind=hl.ind, hl.col=hl.col)
  abline(v=mean(sim162$trans$proj[,1]), lty=2, col="grey60")
  abline(h=mean(sim162$trans$proj[,2]), lty=2, col="grey60")
 mtext("(F) E434K-ATP (trans)", side=3, line=line, cex=mtext.cex, at=xlim[1]-at.offset, adj=0)

conf.plot( sim161$cis$proj, pc.xray, mtext="", xlim=xlim, ylim=ylim,
            hl.ind=hl.ind, hl.col=hl.col)
  abline(v=mean(sim161$cis$proj[,1]), lty=2, col="grey60")
  abline(h=mean(sim161$cis$proj[,2]), lty=2, col="grey60")
mtext("(G) E434K-APO (cis)", side=3, line=line, cex=mtext.cex, at=xlim[1]-at.offset, adj=0)

conf.plot( sim161$trans$proj, pc.xray, mtext="", xlim=xlim, ylim=ylim,
            hl.ind=hl.ind, hl.col=hl.col)
  abline(v=mean(sim161$trans$proj[,1]), lty=2, col="grey60")
  abline(h=mean(sim161$trans$proj[,2]), lty=2, col="grey60")
 mtext("(H) E434K-APO (trans)", side=3, line=line, cex=mtext.cex, at=xlim[1]-at.offset, adj=0)





conf.plot( sim151$cis$proj, pc.xray, mtext="", xlim=xlim, ylim=ylim,
            hl.ind=hl.ind, hl.col=hl.col)
  abline(v=mean(sim151$cis$proj[,1]), lty=2, col="grey60")
  abline(h=mean(sim151$cis$proj[,2]), lty=2, col="grey60")
 mtext("(I) E461K-ATP (cis)", side=3, line=line, cex=mtext.cex, at=xlim[1]-at.offset, adj=0)

conf.plot( sim151$trans$proj, pc.xray, mtext="", xlim=xlim, ylim=ylim,
            hl.ind=hl.ind, hl.col=hl.col)
  abline(v=mean(sim151$trans$proj[,1]), lty=2, col="grey60")
  abline(h=mean(sim151$trans$proj[,2]), lty=2, col="grey60")
  mtext("(J) E461K-ATP (trans)", side=3, line=line, cex=mtext.cex, at=xlim[1]-at.offset, adj=0)

conf.plot( sim150$cis$proj, pc.xray, mtext="", xlim=xlim, ylim=ylim,
            hl.ind=hl.ind, hl.col=hl.col)
  abline(v=mean(sim150$cis$proj[,1]), lty=2, col="grey60")
  abline(h=mean(sim150$cis$proj[,2]), lty=2, col="grey60")
mtext("(K) E461K-APO (cis)", side=3, line=line, cex=mtext.cex, at=xlim[1]-at.offset, adj=0)

conf.plot( sim150$trans$proj, pc.xray, mtext="", xlim=xlim, ylim=ylim,
            hl.ind=hl.ind, hl.col=hl.col)
  abline(v=mean(sim150$trans$proj[,1]), lty=2, col="grey60")
  abline(h=mean(sim150$trans$proj[,2]), lty=2, col="grey60")
 mtext("(L) E461K-APO (trans)", side=3, line=line, cex=mtext.cex, at=xlim[1]-at.offset, adj=0)

dev.off()





by=150
inds=seq(1,3500,by=by)
t.test(sim116$cis$proj[inds,1], sim129$cis$proj[inds,1])
t.test(sim116$trans$proj[inds,1], sim129$trans$proj[inds,1])

inds2=seq(1,2716,by=by)
inds1=seq(1,3500,by=by)
t.test(sim161$cis$proj[inds1,1], sim162$cis$proj[inds2,1])
t.test(sim161$trans$proj[inds1,1], sim162$trans$proj[inds2,1])

inds=seq(1,3500,by=by)
t.test(sim150$cis$proj[inds,1], sim151$cis$proj[inds,1])
t.test(sim150$trans$proj[inds,1], sim151$trans$proj[inds,1])