# NOT RUN {
##-- Generate a small kinesin alignment and read corresponding structures
pdbfiles <- get.pdb(c("1bg2","2ncd","1i6i","1i5s"), URLonly=TRUE)
pdbs <- pdbaln(pdbfiles)
##-- Find 'core' positions
core <- core.find(pdbs)
plot(core)
##-- Fit on these relatively invarient subset of positions
core.inds <- print(core)
xyz <- pdbfit(pdbs, core.inds, outpath="corefit_structures")
##-- Compare to fitting on all equivalent positions
xyz2 <- pdbfit(pdbs)
## Note that overall RMSD will be higher but RMSF will
## be lower in core regions, which may equate to a
## 'better fit' for certain applications
gaps <- gap.inspect(pdbs$xyz)
rmsd(xyz[,gaps$f.inds])
rmsd(xyz2[,gaps$f.inds])
plot(rmsf(xyz[,gaps$f.inds]), typ="l", col="blue", ylim=c(0,9))
points(rmsf(xyz2[,gaps$f.inds]), typ="l", col="red")
# }
# NOT RUN {
# }
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