| read.fasta.pdb {bio3d} | R Documentation |
Read aligned PDB structures and store their C-alpha atom data, including xyz coordinates, residue numbers, residue type and B-factors.
read.fasta.pdb(aln, pdb.path = "", pdbext = "", ...)
aln |
an alignment data structure obtained with
read.fasta. |
pdb.path |
path to PDB files. |
pdbext |
the file name extention of the PDB files. |
... |
other parameters for read.pdb. |
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.
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. |
The sequence character ‘X’ is useful for masking unusual or unknown residues, as it can match any other residue type.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
read.fasta, read.pdb,
core.find, fit.xyz, read.all
# 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,]