Parse PDB using DSR-PDB Library

Question

I'm trying to parse ATOM section of a PDB file. I'm using the dsr-pdb library for this purpose.

I've encountered a problem. This library interprets CD1 atom of ILE residue in the PDB file as AL_CD instead of AL_CD1*. Does it have a particular reason?

It's maybe helpful that within the source code, in Residue_data.cc, there is a mapping between atom lebels:

Atom_fallback_data atom_fallback_data_[]=
      {{Residue::AL_CD1, Residue::AL_CD},
       {Residue::AL_1HA, Residue::AL_HA},
       {Residue::AL_1HB, Residue::AL_HB},
       {Residue::AL_1HD, Residue::AL_HD},
       {Residue::AL_1HE, Residue::AL_HE},
       {Residue::AL_1HZ, Residue::AL_HZ},
       //{Residue::AL_1HH, Residue::AL_HH},
       {Residue::AL_1HD1, Residue::AL_1HD},
       {Residue::AL_2HD1, Residue::AL_2HD},
       {Residue::AL_3HD1, Residue::AL_3HD},
       {Residue::AL_INVALID, Residue::AL_INVALID}};

It means that AL_CD1 is deliberately converted to AL_CD or for example AL_1HA to AL_HA.

Thanks.

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• In general, in dsr-pdb library, AL_X is the atom label of atom X.

Answer 1

Isoleucine only has one delta carbon, which we can just call CD. But it seems like some PDB files still name it CD1, and hence programs map CD1 to CD in this case. (E.g. see this tutorial where this practice is shown.)