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pharmai / plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

Home Page:http://plip.biotec.tu-dresden.de

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Segmentation error with pdb files:

sgrannem opened this issue · comments

commented

Describe the bug
When I run plip in the command line with a specific pdb file it crashes due to a segmentation error.
I cannot really figure out where the error comes from.

To Reproduce
Steps to reproduce the behaviour:

Using a downloaded pdb file:

% plip -f 5o9z.pdb
2022-12-06 09:51:40,013 [INFO] [plipcmd.py:124] plip.plipcmd: Protein-Ligand Interaction Profiler (PLIP) 2.2.2
2022-12-06 09:51:40,013 [INFO] [plipcmd.py:125] plip.plipcmd: brought to you by: PharmAI GmbH (2020-2021) - www.pharm.ai - hello@pharm.ai
2022-12-06 09:51:40,013 [INFO] [plipcmd.py:126] plip.plipcmd: please cite: Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294
2022-12-06 09:51:40,013 [INFO] [plipcmd.py:49] plip.plipcmd: starting analysis of 5o9z.pdb
zsh: segmentation fault plip -f 5o9z.pdb

Asking plip to download the pdb file:

% plip -i 5o9z
2022-12-06 10:38:56,203 [INFO] [plipcmd.py:124] plip.plipcmd: Protein-Ligand Interaction Profiler (PLIP) 2.2.2
2022-12-06 10:38:56,203 [INFO] [plipcmd.py:125] plip.plipcmd: brought to you by: PharmAI GmbH (2020-2021) - www.pharm.ai - hello@pharm.ai
2022-12-06 10:38:56,203 [INFO] [plipcmd.py:126] plip.plipcmd: please cite: Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294
2022-12-06 10:38:58,439 [INFO] [plipcmd.py:99] plip.plipcmd: file downloaded as ./5o9z.pdb
2022-12-06 10:38:58,439 [INFO] [plipcmd.py:49] plip.plipcmd: starting analysis of 5o9z.pdb
zsh: segmentation fault plip -i 5o9z

Expected behavior
[A clear and concise description of what you expected to happen.](zsh: segmentation fault plip -i 5o9z)

Screenshots
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Desktop (please complete the following information):

  • OS: [e.g. iOS]

MacOS Ventura 13.0.1 (22A400)
MacBook Pro 2.3 GHz 8-core i9
64 GB of RAM

300GB of disk space still available.

commented

Hi sgrannem,

most likely this error comes from OpenBabel. We've seen these kind of errors before. Especially when parsing large CryoEM structures. If this is true there is nothing much we can do about it. Can you split your structure before processing with PLIP and use a local file instead of letting PLIP download it?