bio3d (version 2.1-3)

read.all: Read Aligned Structure Data

Description

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

Usage

read.all(aln, prefix = "", pdbext = "", sel = 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.

sel

a selection string detailing the atom type data to store (see function store.atom)

...

other parameters for read.pdb.

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.
• all
  numeric matrix of aligned equalvelent atom coordinates.
• all.elety
  numeric matrix of aligned atom element types.
• all.resid
  numeric matrix of aligned three-letter residue codes.
• all.resno
  numeric matrix of aligned residue numbers.

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 file mypdbdir/1bg2.pdb should have the identifer mypdbdir/1bg2.pdb or 1bg2 if input prefix and pdbext equal mypdbdir/ and pdb. See the 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.

References

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

See Also

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

Examples

# still working on speeding this guy up
cat("")
## Read sequence alignment
file <- system.file("examples/kif1a.fa",package="bio3d")
aln  <- read.fasta(file)

## Read aligned PDBs storing all data for 'sel'
sel <- c("N", "CA", "C", "O", "CB", "*G", "*D",  "*E", "*Z")
pdbs <- read.all(aln, sel=sel)

atm <- colnames(pdbs$all)
ca.ind  <- which(atm == "CA")
core <- core.find(pdbs)
core.ind <- c( matrix(ca.ind, nrow=3)[,core$c0.5A.atom] )

## Fit structures
nxyz <- fit.xyz(pdbs$all[1,], pdbs$all,
               fixed.inds  = core.ind,
               mobile.inds = core.ind)

ngap.col <- gap.inspect(nxyz)

#npc.xray <- pca.xyz(nxyz[ ,ngap.col$f.inds])

#a <- mktrj.pca(npc.xray, pc=1, file="pc1-all.pdb",
#               elety=pdbs$all.elety[1,unique( ceiling(ngap.col$f.inds/3) )],
#               resid=pdbs$all.resid[1,unique( ceiling(ngap.col$f.inds/3) )],
#               resno=pdbs$all.resno[1,unique( ceiling(ngap.col$f.inds/3) )] )