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PDB-REDO / dssp

Application to assign secondary structure to proteins
BSD 2-Clause "Simplified" License
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dssp is only returned for the first chain_id in a .cif model #11

Closed tueboesen closed 3 years ago

tueboesen commented 3 years ago

I just reported this as an issue in biopython here: https://github.com/biopython/biopython/issues/3505 but after looking closer at it, I think it might actually be an issue in dssp rather than biopython.

The issue is that when I run the dssp on the file: '2mys.cif', which contains 3 chain_ids 'A','B','C' then I only get the dssp results from the first chain_id, 'A', but not for the other two chains, which I believe I should be getting.

The structure can be found here: https://www.rcsb.org/structure/2MYS

drlemmus commented 3 years ago

The problem is that chains B and C only contain coordinates for the CA atoms. Therefore no secondary structure assignment is possible for those chains using the DSSP algorithm. So it's not a bug as such, but we will look at improving the verbose output to make clear why it doesn't run on these protein chains.