PDB File Coordinate Superposition
Protein Databank Bank file coordinate superposition with the Kabsch algorithm.
pdbfit(...) ## S3 method for class 'pdb' pdbfit(pdb, inds = NULL, ...) ## S3 method for class 'pdbs' pdbfit(pdbs, inds = NULL, outpath = NULL, ...)
pdb |
a multi-model pdb object of class |
pdbs |
a list of class |
inds |
a list object with a ‘xyz’ component with indices
that selects the coordinate positions (in terms of x, y and z
elements) upon which fitting should be based. This defaults to all
equivalent non-gap positions for function |
outpath |
character string specifing the output directory for optional coordinate file output. Note that full files (i.e. all atom files) are written, seebelow. |
... |
extra arguments passed to |
The function pdbfit is a wrapper for the function
fit.xyz, wherein full details of the superposition procedure
are documented.
Input to pdbfit.pdbs should be a list object obtained with the
function read.fasta.pdb or pdbaln. See
the examples below.
For function pdbfit.pdb the input should be a multi-model
pdb object with multiple (>1) frames in the ‘xyz’
component.
The reference frame for supperposition (i.e. the fixed structure to
which others are superposed) is the first entry in the input
"pdbs" object. For finer control use fit.xyz.
Returns moved coordinates.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
Kabsch Acta Cryst (1978) A34, 827–828.
## Not run:
#files <- get.pdb(c("4q21","5p21"), URLonly=TRUE)
files <- get.pdb(c("4q21","5p21"), path=tempdir(), overwrite=TRUE)
pdbs <- pdbaln(files)
xyz <- pdbfit(pdbs)
# Superpose again this time outputing all-atom PDBs to disc
#xyz <- pdbfit( pdbs, outpath="fitted" )
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.