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SBRG / ssbio

A Python framework for structural systems biology
http://ssbio.readthedocs.io/en/latest/
MIT License
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Problematic PDB files #5

Closed nmih closed 7 years ago

nmih commented 7 years ago

The best_structures API returns chains that are seemingly not present in these files. Find out why get_pdb_seqs doesn't have these chains. These look to be all mmCIF structures.

WARNING:ssbio.pipeline.gempro:5iqr: chain 8 not found in structure!
WARNING:ssbio.pipeline.gempro:5l3p: chain z not found in structure!
WARNING:ssbio.pipeline.gempro:5kpw: chain 33 not found in structure!
WARNING:ssbio.pipeline.gempro:5kpx: chain 33 not found in structure!
WARNING:ssbio.pipeline.gempro:5kpv: chain 33 not found in structure!
nmih commented 7 years ago

This was related to a Biopython bug which used a different field for chain IDs when parsing mmCIF files. See https://github.com/biopython/biopython/pull/800. Fixed with newest Biopython version and also within the ssbio package now.