atom.select(pdb, "backbone")

[Lars Skjærven]

function atom.select currently returns all atoms with name N,CA,C,O. e.g. a bunch of water molecules are returned in the following example (129 C-alpha atoms):

pdb = read.pdb("1hel")
sel = atom.select(pdbfull, "back")
trim.pdb(pdb, sel)


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

   Total Models#: 1
     Total Atoms#: 701,  XYZs#: 2103  Chains#: 1  (values: A)

     Protein Atoms#: 516  (residues/Calpha atoms#: 129)
     Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

     Non-protein/nucleic Atoms#: 185  (residues: 185)
     Non-protein/nucleic resid values: [HOH (185) ]

   Protein sequence:
      KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
      RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
      QAWIRGCRL

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

[Xinqiu Yao]

Good spot! We need to add "prot.aa" to the amino acid field. Have done it with the latest commit

pdb = read.pdb("1hel")
sel = atom.select(pdb, "back")
trim.pdb(pdb, sel)


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

   Total Models#: 1
     Total Atoms#: 516,  XYZs#: 1548  Chains#: 1  (values: A)

     Protein Atoms#: 516  (residues/Calpha atoms#: 129)
     Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

     Non-protein/nucleic Atoms#: 0  (residues: 0)
     Non-protein/nucleic resid values: [ () ]

   Protein sequence:
      KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
      RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
      QAWIRGCRL

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

tail(trim.pdb(pdb, sel)$atom)

    type eleno elety  alt resid chain resno insert       x      y     z o     b
984 ATOM   984     C <NA>   ARG     A   128   <NA> -15.116 19.387 4.645 1 19.23
985 ATOM   985     O <NA>   ARG     A   128   <NA> -14.626 18.345 5.078 1 29.24
993 ATOM   993     N <NA>   LEU     A   129   <NA> -15.775 20.226 5.404 1 22.75
994 ATOM   994    CA <NA>   LEU     A   129   <NA> -15.976 19.869 6.811 1 33.38
995 ATOM   995     C <NA>   LEU     A   129   <NA> -17.449 19.906 7.141 1 72.70
996 ATOM   996     O <NA>   LEU     A   129   <NA> -18.191 20.465 6.277 1 49.87
    segid elesy charge
984  <NA>     C   <NA>
985  <NA>     O   <NA>
993  <NA>     N   <NA>
994  <NA>     C   <NA>
995  <NA>     C   <NA>
996  <NA>     O   <NA>

[Barry Grant]

Looks to be solved.