Printing Core Positions and Returning Indices

Print method for core.find objects.

# S3 method for core
print(x, vol = NULL, ...)

Arguments

x	a list object obtained with the function core.find.
vol	the maximal cumulative volume value at which core positions are detailed.
...	additional arguments to ‘print’.

Value

Returns a three component list of indices:

atom

atom indices of core positions

xyz

xyz indices of core positions

resno

residue numbers of core positions

References

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

Author

Barry Grant

Note

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

See also

core.find, plot.core

Examples

if (FALSE) {
##-- 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, vol=0.5)

print(core, vol=0.7)
print(core, vol=1.0)

}