bio3d (version 2.1-2)

print.core: Printing Core Positions and Returning Indices

Description

Print method for core.find objects.

Usage

## S3 method for class '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.

See Also

core.find, plot.core

Examples

##-- 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)