bio3d read.pdb function

[Former user]

Hi, I am reading a pdb file using read.pdb function. On the screen I can see the sequence but when I try to use it as ax axis label for a plot, I failed.

> a <- read.pdb("/scratch/ukg-030-aa/tugba/frames/tetramer_imp_cot/inputfiles/step1_pdbreader.pdb")
a
> a

 Call:  read.pdb(file = "/scratch/ukg-030-aa/tugba/frames/tetramer_imp_cot/inputfiles/step1_pdbreader.pdb")

   Total Models#: 1
     Total Atoms#: 8228,  XYZs#: 24684  Chains#: 1  (values: P)

     Protein Atoms#: 8228  (residues/Calpha atoms#: 856)
     Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

     Non-protein/nucleic Atoms#: 0  (residues: 0)
     Non-protein/nucleic resid values: [ none ]

   Protein sequence:
      MSQSGEDLHSPTYLSWRKLQLSRAKLKASSKTSALLSGFAMVAMVEVQLDHDTNVPPGML
      IAFAICTTLLVAVHMLALMISTCILPNIETVSNLHSISLVHESPHERLHWYIETAWAFST
      LLGLILFLLEIAILCWVKFYDLSRRAAWSATVVLIPVMIIFMAFAIHFYRSLVSHKYEVT
      VSGIRELEMLKEQMEQDHLEHHNNIRNNGEGEEFMSQSGEDLHSP...<cut>...GEEF

+ attr: atom, helix, sheet, seqres, xyz,
        calpha, remark, call
> a$seqres
NULL

Is there a way to get the sequence shown here as a list? and why does seqres return NULL? Thanks in advance

[Barry Grant]

The read.pdb() function returns a PDB object not a sequence. What you see printed out to screen when you type the name of your PDB object is a summary of its contents (actually generated from the print.pdb() function.

If you want the sequence as a vector call the pdbseq() function with your PDB object as input.