trim {bio3d}

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(...)

## S3 method for class 'pdb'
trim(pdb, ..., inds = NULL, sse = TRUE)

Arguments

pdb

a PDB structure object obtained from read.pdb.

...

additional arguments passed to atom.select. If inds is also provided, these arguments will be ignored.

inds

a list object of ATOM and XYZ indices as obtained from atom.select. If NULL, atom selection will be obtained from calling atom.select(pdb, ...).

sse

logical, if ‘FALSE’ helix and sheet components are omitted from output.

Details

This is a basic utility function for creating a new PDB object based on a selection of atoms.

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.

xyz.models

a numeric matrix of ATOM coordinate data for multi-model PDB files.

calpha

logical vector with length equal to nrow(atom) with TRUE values indicating a C-alpha “elety”.

Note

het and seqres list components are returned unmodified.

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, Lars Skjaerven

References

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

For a description of PDB format (version3.3) see:
http://www.wwpdb.org/documentation/format33/v3.3.html. .

See Also

trim.pdbs, trim.xyz, read.pdb, atom.select

Examples

## Not run: 
## Read a PDB file from the RCSB online database
pdb <- read.pdb("1bg2")

## Select calpha atoms
sele <- atom.select(pdb, "calpha")

## Trim PDB
new.pdb <- trim.pdb(pdb, inds=sele)

## Or, simply
#new.pdb <- trim.pdb(pdb, "calpha")

## Write to file
write.pdb(new.pdb, file="calpha.pdb")

## End(Not run)