read.fasta.pdb(aln, prefix = "", pdbext = "", fix.ali = FALSE,
ncore = 1, nseg.scale = 1, ...)
read.fasta
.$ali
and $resno
, and correct $ali
if they don't match.ncore>1
requires package fit.xyz
.read.pdb
."pdbs"
with the following five
components:aln
, produced with read.fasta
, must
have identifers (i.e. sequence names) that match the PDB file
names. For example the sequence corresponding to the structure
read.fasta
, read.pdb
,
core.find
, fit.xyz
, read.all
# Read sequence alignment
file <- system.file("examples/kif1a.fa",package="bio3d")
aln <- read.fasta(file)
# Read aligned PDBs
pdbs <- read.fasta.pdb(aln)
# Structure/sequence names/ids
basename( pdbs$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)]
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