plot.core {bio3d}R Documentation

Plot Core Fitting Progress

Description

Plots the total ellipsoid volume of core positions versus core size at each iteration of the core finding process.

Usage

plot.core(x, y = NULL, type = "h", main = "", sub = "", xlim = NULL, ylim = NULL, xlab = "Core Size (Number of Residues)", ylab = "Total Ellipsoid Volume (Angstrom^3)", axes = TRUE, ann = par("ann"), col = par("col"), ...)

Arguments

x a list object obtained with the function core.find from which the ‘volume’ component is taken as the x coordinates for the plot.
y the y coordinates for the plot.
type one-character string giving the type of plot desired.
main a main title for the plot, see also ‘title’.
sub a sub-title for the plot.
xlim the x limits of the plot.
ylim the y limits of the plot.
xlab a label for the x axis.
ylab a label for the y axis.
axes a logical value indicating whether both axes should be drawn.
ann a logical value indicating whether the default annotation (title and x and y axis labels) should appear on the plot.
col The colors for lines and points. Multiple colours can be specified so that each point is given its own color. If there are fewer colors than points they are recycled in the standard fashion.
... extra plotting arguments.

Value

Called for its effect.

Note

The produced plot can be useful for deciding on the core/non-core boundary.

Author(s)

Barry Grant

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

See Also

core.find, print.core

Examples

## Not run: 
##-- Read kinesin alignment and structures
aln <- read.fasta(system.file("examples/kinesin_xray.fa",package="bio3d"))
pdb.path = system.file("examples/",package="bio3d")
pdbs <- read.fasta.pdb(aln, pdb.path = pdb.path, pdbext = ".ent")

## Find core
core <- core.find(pdbs,
                  #write.pdbs = TRUE,
                  verbose=TRUE)
## End(Not run)

##-- OR read previously saved kinesin data
data(kinesin)
attach(kinesin)

col=rep("black", length(core$volume))
col[core$volume<2]="pink"; col[core$volume<1]="red"
plot(core, col=col)

print(core)

[Package bio3d version 1.0-5 Index]