bio3d (version 2.1-3)

pdbfit: PDB File Coordinate Superposition

Description

Protein Databank Bank file coordinate superposition with the Kabsch algorithm.

Usage

pdbfit(pdbs, inds = NULL, outpath = NULL, ...)

Arguments

pdbs

a list of class "pdbs" containing PDB file data, as obtained from read.fasta.pdb or pdbaln.

inds

a vector of indices that selects the coordinate positions, in terms of x, y and z elements, upon which fitting should be based. This defults to all equivalent non-gap positions.

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 fit.xyz function.

Value

• Returns moved coordinates.

Details

The function pdbfit is a wrapper for the function fit.xyz, wherein full details of the superposition procedure are documented.

Input to this function should be a list object obtained with the function read.fasta.pdb or pdbaln. See the examples below.

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.

References

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

Kabsch Acta Cryst (1978) A34, 827--828.

See Also

pdbaln, read.fasta.pdb, fit.xyz, rmsd, read.pdb

Examples

#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 PDBs
#xyz <- pdbaln( files, outpath="fitted" )