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samirelanduk / atomium

Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)
https://atomium.bio
MIT License
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the "add_secondary_structure_to_polymers" function in the mmcif.py module only recognises single-letter chain identifiers #34

Closed FunkTipp closed 3 years ago

FunkTipp commented 3 years ago

For Bug Reports

the "add_secondary_structure_to_polymers" function in the mmcif.py module only recognises single-letter chain identifiers

Problem

cryoEM derived mmcif files often have multi-litter chain identifiers, those chains are not recognised and secondary structure information is not forwarded to downstream functions

the reason can be found in line 567: <chain = model["polymer"].get(segment[0][0])> it should be exchanged by: <chain = model["polymer"].get(segment[0].split('.')[0])> or similar behaving commands to allow multi-letter chain identifiers

Python Version/Operating System

atomimuim 1.0.6

samirelanduk commented 3 years ago

Thanks for spotting this - I'll publish a fix this week.

samirelanduk commented 3 years ago

This should be fixed now in 1.0.10 (just released).