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haddocking / pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.
https://haddocking.github.io/pdb-tools/
Apache License 2.0
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pdb_selchain is not able to extract a chain with lowercase chain ID when the uppercase is present #41

Closed DarioMarzella closed 4 years ago

DarioMarzella commented 4 years ago

Description When running pdb_selchain on a PDB file containing both uppercase chain IDs and lowercase chain IDs and trying to exctract only a chain with a lowercase ID, pdb_selchain will instead extract the chain with the uppercase ID character.

To Reproduce Sample pdb: 4L29.pdb Output: 4L29_m.pdb will have only chain 'M'

pdb_selchain -m 4L29.pdb > 4L29_m.pdb

Expected behavior The output file should have only chain 'm' (lowercase), not chain 'M' (uppercase).

Desktop:

joaomcteixeira commented 4 years ago

Hi @DarioMarzella This issue was also reported in #39 and solved in #40. Though this update was not added to PyPI, which currently has version 2.0.0 (some commits behind the master branch).

If you want to use this functionality right away, you should reinstall pdb-tools from the master branch of this git repository:

pip install git+git://github.com/haddocking/pdb-tools.git

I will open a new issue to require update of the PyPI version.