read.pdcBD(file, maxlines = 50000, multi = FALSE, rm.insert = FALSE, rm.alt = TRUE, verbose = TRUE)
Read a pdcBD PQR coordinate file.
maxlines may require increasing for some large multi-model files.
The preferred means of reading such data is via binary DCD format
trajectory files (see the read.dcd function).
"pdb" with the following components:
atom). nrow(atom)
with TRUE values indicating a C-alpha “elety”. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
For a description of PDB format (version3.3) see: http://www.wwpdb.org/documentation/format33/v3.3.html.
For both atom and het list components the column names can be
used as a convenient means of data access, namely:
Atom serial number “eleno” ,
Atom type “elety”,
Alternate location indicator “alt”,
Residue name “resid”,
Chain identifier “chain”,
Residue sequence number “resno”,
Code for insertion of residues “insert”,
Orthogonal coordinates “x”,
Orthogonal coordinates “y”,
Orthogonal coordinates “z”,
Occupancy “o”, and
Temperature factor “b”.
See examples for further details.
# PDB server connection required - testing excluded # Read a PDB file pdb <- read.pdb( "1bg2" )Note: Accessing on-line PDB file# Print data for the first atom pdb$atom[1,]type eleno elety alt resid chain resno insert x y z o b 1 ATOM 1 N <NA> ASP A 3 <NA> 43.743 -2.106 39.408 1 100 segid elesy charge 1 <NA> N <NA># Look at the first het atom pdb$het[1,]NULL# Print some coordinate data pdb$atom[1:20, c("x","y","z")]x y z 1 43.743 -2.106 39.408 2 45.053 -2.661 39.856 3 45.305 -2.401 41.340 4 46.119 -3.083 41.957 5 46.204 -2.067 39.034 6 45.912 -2.039 37.542 7 45.455 -3.066 36.993 8 46.136 -0.978 36.920 9 44.627 -1.402 41.903 10 44.791 -1.079 43.319 11 44.313 -2.242 44.183 12 45.079 -2.800 44.969 13 44.015 0.191 43.679 14 44.010 0.584 45.160 15 45.430 0.779 45.663 16 43.202 1.850 45.351 17 43.039 -2.590 44.037 18 42.451 -3.691 44.790 19 41.508 -4.495 43.904 20 41.084 -5.588 44.275# Print C-alpha coordinates (can also use 'atom.select') ##pdb$xyz[pdb$calpha, c("resid","x","y","z")] # Print SSE data (for helix and sheet) pdb$helix$start 20 58 67 91 107 176 197 256 277 281 306 $end 25 65 74 95 122 191 203 269 279 288 321 $chain [1] "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" $type [1] "1" "1" "1" "1" "1" "1" "1" "1" "5" "1" "5"pdb$sheet$start50 8 295 79 222 205 126 171 32 38 44 135 141 155 163# Print SEQRES data pdb$seqresA A A A A A A A A A A A A "MET" "ALA" "ASP" "LEU" "ALA" "GLU" "CYS" "ASN" "ILE" "LYS" "VAL" "MET" "CYS" A A A A A A A A A A A A A "ARG" "PHE" "ARG" "PRO" "LEU" "ASN" "GLU" "SER" "GLU" "VAL" "ASN" "ARG" "GLY" A A A A A A A A A A A A A "ASP" "LYS" "TYR" "ILE" "ALA" "LYS" "PHE" "GLN" "GLY" "GLU" "ASP" "THR" "VAL" A A A A A A A A A A A A A "VAL" "ILE" "ALA" "SER" "LYS" "PRO" "TYR" "ALA" "PHE" "ASP" "ARG" "VAL" "PHE" A A A A A A A A A A A A A "GLN" "SER" "SER" "THR" "SER" "GLN" "GLU" "GLN" "VAL" "TYR" "ASN" "ASP" "CYS" A A A A A A A A A A A A A "ALA" "LYS" "LYS" "ILE" "VAL" "LYS" "ASP" "VAL" "LEU" "GLU" "GLY" "TYR" "ASN" A A A A A A A A A A A A A "GLY" "THR" "ILE" "PHE" "ALA" "TYR" "GLY" "GLN" "THR" "SER" "SER" "GLY" "LYS" A A A A A A A A A A A A A "THR" "HIS" "THR" "MET" "GLU" "GLY" "LYS" "LEU" "HIS" "ASP" "PRO" "GLU" "GLY" A A A A A A A A A A A A A "MET" "GLY" "ILE" "ILE" "PRO" "ARG" "ILE" "VAL" "GLN" "ASP" "ILE" "PHE" "ASN" A A A A A A A A A A A A A "TYR" "ILE" "TYR" "SER" "MET" "ASP" "GLU" "ASN" "LEU" "GLU" "PHE" "HIS" "ILE" A A A A A A A A A A A A A "LYS" "VAL" "SER" "TYR" "PHE" "GLU" "ILE" "TYR" "LEU" "ASP" "LYS" "ILE" "ARG" A A A A A A A A A A A A A "ASP" "LEU" "LEU" "ASP" "VAL" "SER" "LYS" "THR" "ASN" "LEU" "SER" "VAL" "HIS" A A A A A A A A A A A A A "GLU" "ASP" "LYS" "ASN" "ARG" "VAL" "PRO" "TYR" "VAL" "LYS" "GLY" "CYS" "THR" A A A A A A A A A A A A A "GLU" "ARG" "PHE" "VAL" "CYS" "SER" "PRO" "ASP" "GLU" "VAL" "MET" "ASP" "THR" A A A A A A A A A A A A A "ILE" "ASP" "GLU" "GLY" "LYS" "SER" "ASN" "ARG" "HIS" "VAL" "ALA" "VAL" "THR" A A A A A A A A A A A A A "ASN" "MET" "ASN" "GLU" "HIS" "SER" "SER" "ARG" "SER" "HIS" "SER" "ILE" "PHE" A A A A A A A A A A A A A "LEU" "ILE" "ASN" "VAL" "LYS" "GLN" "GLU" "ASN" "THR" "GLN" "THR" "GLU" "GLN" A A A A A A A A A A A A A "LYS" "LEU" "SER" "GLY" "LYS" "LEU" "TYR" "LEU" "VAL" "ASP" "LEU" "ALA" "GLY" A A A A A A A A A A A A A "SER" "GLU" "LYS" "VAL" "SER" "LYS" "THR" "GLY" "ALA" "GLU" "GLY" "ALA" "VAL" A A A A A A A A A A A A A "LEU" "ASP" "GLU" "ALA" "LYS" "ASN" "ILE" "ASN" "LYS" "SER" "LEU" "SER" "ALA" A A A A A A A A A A A A A "LEU" "GLY" "ASN" "VAL" "ILE" "SER" "ALA" "LEU" "ALA" "GLU" "GLY" "SER" "THR" A A A A A A A A A A A A A "TYR" "VAL" "PRO" "TYR" "ARG" "ASP" "SER" "LYS" "MET" "THR" "ARG" "ILE" "LEU" A A A A A A A A A A A A A "GLN" "ASP" "SER" "LEU" "GLY" "GLY" "ASN" "CYS" "ARG" "THR" "THR" "ILE" "VAL" A A A A A A A A A A A A A "ILE" "CYS" "CYS" "SER" "PRO" "SER" "SER" "TYR" "ASN" "GLU" "SER" "GLU" "THR" A A A A A A A A A A A A A "LYS" "SER" "THR" "LEU" "LEU" "PHE" "GLY" "GLN" "ARG" "ALA" "LYS" "THR" "ILE"# Renumber residues nums <- as.numeric(pdb$atom[,"resno"]) pdb$atom[,"resno"] <- nums - (nums[1] - 1) # Write out renumbered PDB file #write.pdb(pdb=pdb,file="eg.pdb")