read.fasta.pdb {bio3d}R Documentation

Read Aligned Structure Data

Description

Read aligned PDB structures and store their C-alpha atom data, including xyz coordinates, residue numbers, residue type and B-factors.

Usage

read.fasta.pdb(aln, pdb.path = "", pdbext = ".pdb")

Arguments

aln an alignment data structure obtained with read.fasta.
pdb.path path to PDB files.
pdbext the file name extention of the PDB files.

Details

The input aln, produced with read.fasta, must have identifers (i.e. sequence names) that match the PDB file names. For example the sequence corresponding to the structure “1bg2.pdb” should have the identifer ‘1bg2’. See examples below.

Sequence miss-matches will generate errors. Thus, care should be taken to ensure that the sequences in the alignment match the sequences in their associated PDB files.

Value

Returns a list of class "3dalign" with the following five components:

xyz numeric matrix of aligned C-alpha coordinates.
resno character matrix of aligned residue numbers.
b numeric matrix of aligned B-factor values.
chain character matrix of aligned chain identifiers.
id character vector of PDB sequence/structure names.
ali character matrix of aligned sequences.

Note

The sequence character ‘X’ is useful for masking unusual or unknown residues, as it can match any other residue type.

Author(s)

Barry Grant

References

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

See Also

read.fasta, read.pdb, core.find, fit.xyz, read.all

Examples

# Read sequence alignment
file <- system.file("examples/kif1a.fa",package="bio3d")
aln  <- read.fasta(file)

# Read aligned PDBs
pdb.path = system.file("examples",package="bio3d")
pdbs <- read.fasta.pdb(aln, pdb.path = pdb.path, pdbext = ".ent")

# Structure/sequence names/ids
pdbs$id

# Alignment positions 335 to 339
pdbs$ali[,335:339]
pdbs$resno[,335:339]
pdbs$b[,335:339]

# Alignment C-alpha coordinates for first structure
pdbs$xyz[1,]


[Package bio3d version 1.0-5 Index]