R: PDB File Coordinate Superposition

pdbfit {bio3d} | R Documentation

## PDB File Coordinate Superposition

### Description

Protein Databank Bank file coordinate superposition with the Kabsch algorithm.

### Usage

    pdbfit(...)

    ## S3 method for class 'pdb'
    pdbfit(pdb, inds = NULL, ...)

    ## S3 method for class 'pdbs'
    pdbfit(pdbs, inds = NULL, outpath = NULL, ...)

### Arguments

`pdb` | a multi-model pdb object of class `"pdb"`, as obtained from `read.pdb`.
`pdbs` | a list of class `"pdbs"` containing PDB file data, as obtained from `read.fasta.pdb` or `pdbaln`.
`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 `pdbfit.pdbs`, and to all calpha atoms for function `pdbfit.pdb`.
`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.

### Details

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`.

### Value

Returns moved coordinates.

### Author(s)

Barry Grant

### 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

    ## 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)

[Package bio3d version 2.4-2 Index]