How to subset a PDB by range of residue

I have the attached PDB file.

The PDB read out with this code:

library(bio3d)
pdb_file <- "test.pdb"
pdb <- read.pdb(pdb_file)
pdb

looks like this:

    Call:  read.pdb(file = pdb_file)

   Total Models#: 1
     Total Atoms#: 712,  XYZs#: 2136  Chains#: 1  (values: A)

     Protein Atoms#: 712  (residues/Calpha atoms#: 44)
     Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

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

   Protein sequence:
      MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKK

+ attr: atom, xyz, calpha, call

What I want to do is to extract first 10 amino acid sequenceMGKGDPKKPR from MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKK (full) as PDB.
The final PDB is to include all atoms.

But with this code:

p1_sele <- atom.select(pdb, "protein", chain="A", resno = 1:10)
trim.pdb(pdb, p1_sele)

I only get MGK.

Call:  trim.pdb(pdb = pdb, p1_sele)

   Total Models#: 1
     Total Atoms#: 46,  XYZs#: 138  Chains#: 1  (values: A)

     Protein Atoms#: 46  (residues/Calpha atoms#: 3)
     Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

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

   Protein sequence:
      MGK

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

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What’s the right way to do it?

Comments (9)