Printing Core Positions and Returning Indices
Print method for core.find objects.
## S3 method for class 'core' print(x, vol = NULL, ...)
x |
a list object obtained with the function
|
vol |
the maximal cumulative volume value at which core positions are detailed. |
... |
additional arguments to ‘print’. |
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 |
The produced plot.core function can be useful for deciding on the
core/non-core boundary.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
## 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, vol=0.5)
print(core, vol=0.7)
print(core, vol=1.0)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.