trim.pdb {bio3d}R Documentation

Trim a PDB Object To A Subset of Atoms.

Description

Produce a new smaller PDB object, containing a subset of atoms, from a given larger PDB object.

Usage

trim.pdb(pdb, inds = NULL)

Arguments

pdb a PDB structure object obtained from read.pdb.
inds a list object of ATOM and XYZ indices as obtained from atom.select.

Details

This is a basic utility function for selecting a subset of a PDB object.

Value

Returns a list of class "pdb" with the following components:

atom a character matrix containing all atomic coordinate ATOM data, with a row per ATOM and a column per record type. See below for details of the record type naming convention (useful for accessing columns).
het a character matrix containing atomic coordinate records for atoms within “non-standard” HET groups (see atom).
helix ‘start’, ‘end’ and ‘length’ of H type sse, where start and end are residue numbers “resno”.
sheet ‘start’, ‘end’ and ‘length’ of E type sse, where start and end are residue numbers “resno”.
seqres sequence from SEQRES field.
xyz a numeric vector of ATOM coordinate data.
calpha logical vector with length equal to nrow(atom) with TRUE values indicating a C-alpha “elety”.

Note

For both atom and het list components the column names can be used as a convenient means of data access, namely: Atom serial number “eleno” , Atom type “elety”, Alternate location indicator “alt”, Residue name “resid”, Chain identifier “chain”, Residue sequence number “resno”, Code for insertion of residues “insert”, Orthogonal coordinates “x”, Orthogonal coordinates “y”, Orthogonal coordinates “z”, Occupancy “o”, and Temperature factor “b”. See examples for further details.

Author(s)

Barry Grant

References

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

For a description of PDB format (version2.2) see:
http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/guide2.2_frame.html .

See Also

atom.select, write.pdb, read.dcd, read.fasta.pdb, read.fasta

Examples

## pdb <- read.pdb( get.pdb("5p21", URLonly=TRUE) )
## npdb <- trim.pdb(pdb, inds=atom.select(pdb, "back")
## write.pdb(npdb, file="backboneonly.pdb")

[Package bio3d version 1.0-6 Index]