R: Orient a PDB Structure

orient.pdb {bio3d} | R Documentation

## Orient a PDB Structure

### Description

Center, to the coordinate origin, and orient, by principal axes, the coordinates of a given PDB structure or xyz vector.

### Usage

    orient.pdb(pdb, atom.subset = NULL, verbose = TRUE)

### Arguments

`pdb` | a pdb data structure obtained from `read.pdb` or a vector of ‘xyz’ coordinates.
`atom.subset` | a subset of atom positions to base orientation on.
`verbose` | print dimension details.

### Value

Returns a numeric vector of re-oriented coordinates.

### Note

Centering and orientation can be restricted to a `atom.subset` of atoms.

### Author(s)

Barry Grant

### References

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

### See Also

`read.pdb`, `write.pdb`, `fit.xyz`, `rot.lsq` , `atom.select`

### Examples

    # PDB server connection required - testing excluded

    pdb <- read.pdb( "1bg2" )
    xyz <- orient.pdb(pdb)
    #write.pdb(pdb, xyz = xyz, file = "mov1.pdb")

    # Based on C-alphas
    inds <- atom.select(pdb, "calpha")
    xyz  <- orient.pdb(pdb, atom.subset=inds$atom)
    #write.pdb(pdb, xyz = xyz, file = "mov2.pdb")

    # Based on a central Beta-strand
    inds <- atom.select(pdb, resno=c(224:232), elety='CA')
    xyz  <- orient.pdb(pdb, atom.subset=inds$atom)
    #write.pdb(pdb, xyz = xyz, file = "mov3.pdb")

[Package bio3d version 2.3-3 Index]