[Biopython] Reading PDB files containing multiple copies of the same molecule

[Alister Burt]

Hi João,

Thanks for the quick reply and solution, much appreciated!

Cheers,

Alister

> On 1 Nov 2019, at 23:27, João Rodrigues <j.p.g.l.m.rodrigues at gmail.com> wrote:
> 
> Hi Alister,
> 
> The Biopython parser identifies unique residues based on chain ids. For a quick solution, you can use the pdb_segxchain tool from https://pypi.org/project/pdb-tools/ <https://pypi.org/project/pdb-tools/> to swap the segid to the chain id field. Then re-read using bio.pdb
> 
> Cheers, 
> 
> João 
> 
> A sexta, 1/11/2019, 15:21, Alister Burt <alisterburt at gmail.com <mailto:alisterburt at gmail.com>> escreveu:
> Hi all,
> 
> Apologies if there’s an easy solution to this but a quick google didn’t turn up anything!
> 
> I’m trying to use Bio.PDB.PDBParser.get_structure() to read a pdb file from a collaborator. The file contains multiple copies of the a few different molecules, differentiated by the SEGID entry in columns 73:76 of the file. 
> 
> When trying to read this file I get the following error once for each atom in a chain which was already defined:
> > /Users/alisterburt/anaconda/envs/py37/lib/python3.7/site-packages/Bio/PDB/PDBParser.py:291: PDBConstructionWarning: PDBConstructionException: ('H_POP', 26, ' ') defined twice at line 76812.
> > Exception ignored.
> > Some atoms or residues may be missing in the data structure.
> >   % message, PDBConstructionWarning)
> 
> This means the resulting Structure object only contains one copy of each molecule.
> 
> I know this SEGID entry is not part of the official PDB format, does anyone have a quick solution that will allow me to read in all atoms from this file?
> 
> Thanks in advance,
> 
> Alister
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