read.fasta.pdb: Read Aligned Structure Data

In bio3d: Biological Structure Analysis

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, prefix = "", pdbext = "", fix.ali = FALSE,
             pdblist=NULL, ncore = 1, nseg.scale = 1, progress = NULL, ...)

Arguments

aln	an alignment data structure obtained with read.fasta.
prefix	prefix to aln$id to locate PDB files.
pdbext	the file name extention of the PDB files.
fix.ali	logical, if TRUE check consistence between $ali and $resno, and correct $ali if they don't match.
pdblist	an optional list of pdb objects with sequence corresponding to the alignments in aln. Primarily used through function pdbaln when the PDB objects already exists (avoids reading PDBs from file).
ncore	number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed.
nseg.scale	split input data into specified number of segments prior to running multiple core calculation. See fit.xyz.
progress	progress bar for use with shiny web app.
...	other parameters for read.pdb.

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 "pdbs" 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.
resid	character matrix of aligned 3-letter residue names.
sse	character matrix of aligned helix and strand secondary structure elements as defined in each PDB file.
call	the matched call.

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, pymol.pdbs

Examples

# Redundant testing excluded
try({

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

# Read aligned PDBs
pdbs <- read.fasta.pdb(aln)

# Structure/sequence names/ids
basename( pdbs$id )

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

# Alignment C-alpha coordinates for these positions
pdbs$xyz[, atom2xyz(335:339)]

# See 'fit.xyz()' function for actual coordinate superposition
#  e.g. fit to first structure
# xyz <- fit.xyz(pdbs$xyz[1,], pdbs)
# xyz[, atom2xyz(335:339)]

}, silent=TRUE)
if(inherits(.Last.value, "try-error")) {
   message("Need internet to run the example")
}

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.