Read Aligned Structure Data

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, 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.

References

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

Author

Barry Grant

Note

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

See also

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

Examples

# \donttest{
# Redundant testing excluded

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

# Read aligned PDBs
pdbs <- read.fasta.pdb(aln)
#> pdb/seq: 1   name: http://www.rcsb.org/pdb/files/1bg2.pdb 
#> pdb/seq: 2   name: http://www.rcsb.org/pdb/files/1i6i.pdb 
#>    PDB has ALT records, taking A only, rm.alt=TRUE
#> pdb/seq: 3   name: http://www.rcsb.org/pdb/files/1i5s.pdb 
#>    PDB has ALT records, taking A only, rm.alt=TRUE
#> pdb/seq: 4   name: http://www.rcsb.org/pdb/files/2ncd.pdb 

# Structure/sequence names/ids
basename( pdbs$id )
#> [1] "1bg2.pdb" "1i6i.pdb" "1i5s.pdb" "2ncd.pdb"

# Alignment positions 335 to 339
pdbs$ali[,335:339]
#>                                        [,1] [,2] [,3] [,4] [,5]
#> http://www.rcsb.org/pdb/files/1bg2.pdb "L"  "L"  "F"  "G"  "Q" 
#> http://www.rcsb.org/pdb/files/1i6i.pdb "L"  "R"  "Y"  "A"  "D" 
#> http://www.rcsb.org/pdb/files/1i5s.pdb "L"  "R"  "Y"  "A"  "D" 
#> http://www.rcsb.org/pdb/files/2ncd.pdb "L"  "R"  "F"  "A"  "A" 
pdbs$resid[,335:339]
#>                                        [,1]  [,2]  [,3]  [,4]  [,5] 
#> http://www.rcsb.org/pdb/files/1bg2.pdb "LEU" "LEU" "PHE" "GLY" "GLN"
#> http://www.rcsb.org/pdb/files/1i6i.pdb "LEU" "ARG" "TYR" "ALA" "ASP"
#> http://www.rcsb.org/pdb/files/1i5s.pdb "LEU" "ARG" "TYR" "ALA" "ASP"
#> http://www.rcsb.org/pdb/files/2ncd.pdb "LEU" "ARG" "PHE" "ALA" "ALA"
pdbs$resno[,335:339]
#>                                        [,1] [,2] [,3] [,4] [,5]
#> http://www.rcsb.org/pdb/files/1bg2.pdb  316  317  318  319  320
#> http://www.rcsb.org/pdb/files/1i6i.pdb  345  346  347  348  349
#> http://www.rcsb.org/pdb/files/1i5s.pdb  345  346  347  348  349
#> http://www.rcsb.org/pdb/files/2ncd.pdb  661  662  663  664  665
pdbs$b[,335:339]
#>                                         [,1]  [,2]  [,3]  [,4]  [,5]
#> http://www.rcsb.org/pdb/files/1bg2.pdb 14.99 15.46  9.61 12.16 26.17
#> http://www.rcsb.org/pdb/files/1i6i.pdb 19.27 22.65 23.66 20.76 26.02
#> http://www.rcsb.org/pdb/files/1i5s.pdb 16.08 19.46 16.91 20.48 26.71
#> http://www.rcsb.org/pdb/files/2ncd.pdb 14.01 22.77 31.48 44.88 54.12

# Alignment C-alpha coordinates for these positions
pdbs$xyz[, atom2xyz(335:339)]
#>                                          [,1]    [,2]   [,3]   [,4]    [,5]
#> http://www.rcsb.org/pdb/files/1bg2.pdb 18.880  -4.358 46.825 19.801  -7.246
#> http://www.rcsb.org/pdb/files/1i6i.pdb  4.206  34.360  4.539  3.439  38.005
#> http://www.rcsb.org/pdb/files/1i5s.pdb 16.417 -33.136  4.337 17.452 -36.750
#> http://www.rcsb.org/pdb/files/2ncd.pdb  0.185  37.134 46.308 -0.375  34.180
#>                                          [,6]   [,7]    [,8]   [,9]  [,10]
#> http://www.rcsb.org/pdb/files/1bg2.pdb 44.546 21.449  -4.913 42.020 23.509
#> http://www.rcsb.org/pdb/files/1i6i.pdb  5.403  1.775  37.124  8.670  4.660
#> http://www.rcsb.org/pdb/files/1i5s.pdb  5.131 19.143 -35.570  8.292 15.967
#> http://www.rcsb.org/pdb/files/2ncd.pdb 48.642 -2.386  36.408 50.962 -4.710
#>                                          [,11]  [,12]  [,13]   [,14]  [,15]
#> http://www.rcsb.org/pdb/files/1bg2.pdb  -3.354 44.785 24.545  -6.830 45.885
#> http://www.rcsb.org/pdb/files/1i6i.pdb  34.826  9.548  7.057  37.666  8.763
#> http://www.rcsb.org/pdb/files/1i5s.pdb -33.755  9.354 13.829 -36.723  8.388
#> http://www.rcsb.org/pdb/files/2ncd.pdb  36.941 48.048 -4.498  33.173 47.625

# 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)]

# }