SSE with trim.pdb

> pdb = read.pdb("4wvb")
  Note: Accessing on-line PDB file
  HEADER    HYDROLASE                               05-NOV-14   4WVB               
   PDB has ALT records, taking A only, rm.alt=TRUE
> pdb = trim.pdb(pdb, chain="A")
> plot.bio3d(pdb$atom$b[ pdb$calpha ], sse=pdb)
Error in e[, "start"] : incorrect number of dimensions

> pdb

 Call:  trim.pdb(pdb = pdb, chain = "A")

   Total Models#: 1
     Total Atoms#: 3524,  XYZs#: 10572  Chains#: 1  (values: A)

     Protein Atoms#: 3246  (residues/Calpha atoms#: 394)
     Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

     Non-protein/nucleic Atoms#: 278  (residues: 253)
     Non-protein/nucleic resid values: [ CL (1), GLC (1), HOH (249), MPD (2) ]

   Protein sequence:
      PLRTKAVEVLQRNSRGAFTVPAHGLYPYQWLWDSAFIALGWTQVDWERAWQELLCLFDYG
      QGPDGMLPHIVFHEQSRDYFPGPWGREARAQPATSGITQPPVVATVVRYLYEKDPDRDRA
      RERARYLFPKLLAFHRWLYHARDPYRTGLVVIVHPWESGMDNSPAWDKPLSRVPVEDYDR
      YLSLLYLFRRLEYDPREIYRQSPFKVVDVGFNAILQRANRDLYAL...<cut>...FWTR

+ attr: atom, helix, sheet, seqres, xyz,
        calpha, call

> pdb$helix
$start

  3  33  47 106 120 158 167 170 203 220 234 259 299 304 312 355 371 408 

$end

 15  44  63 118 147 163 169 176 217 228 255 276 303 309 328 369 390 419 

$chain
 [1] "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A"

$type
 [1] "1" "1" "1" "1" "1" "5" "5" "1" "1" "1" "1" "1" "5" "1" "1" "1" "1" "1"

> pdb$sheet
$start

 31  72  97  93 232 287 293 277 283 392 402 

$end

 32  74  98  95 233 288 294 278 284 395 406 

$chain
 [1] "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A"

$sense
 [1] "0"  "-1" "-1" "0"  "0"  "-1" "-1" "0"  "-1" "0"  "-1"
Comments (2)
