[Bioperl-l] More on PDB and chains...

Bernd Web bernd.web at gmail.com
Fri Sep 15 04:57:19 EDT 2006


Hi Brian,

Just to give some PDB accession with multiple models:

1A4T
1A6B
1A6S
2CPS

Structure parser the PDB and looks for a chain. HETATMs in multichain
records do not have a "chain" so end up in the "default" chain. Chain
parsing thus should also take the TER into account. Then the non-chain
HETATMS can be recognized since the follow the TER in the 1 chain
record. I'll check this.

Is anyone else on this list using StructureIO::pdb at all?

Bernd

On 9/14/06, Brian Osborne <osborne1 at optonline.net> wrote:
> Chris and Bernd,
>
> I believe there's more to it than structure->chain->residue->atom, it is
> currently more like entry->structure AKA model->chain->residue->atom. In
> this way one can accommodate macromolecular structures or complexes composed
> of more than 1 protein, each protein capable of having more than one chain.
>
> From Entry.pm:
>
> This object stores a whole Bio::Structure entry. It can consist of one
> or more models (L<Bio::Structure::Model>), which in turn consist of one
> or more chains (L<Bio::Structure::Chain>). A chain is composed of residues
> (L<Bio::Structure::Residue>) and a residue consists of atoms
> (L<Bio::Structure::Atom>).
>
> My understanding is that multiple models in a single PDB file are separated
> by ENDMDL - Bernd, do you know of a multi-model PDB entry?
>
> However, Entry is handling all kinds of different functions e.g. getting and
> setting residues. I agree that this is unconventional.
>
> Brian O.


More information about the Bioperl-l mailing list