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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
http://plip.biotec.tu-dresden.de
GNU General Public License v2.0
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Segmentation error with pdb files: #137

Open sgrannem opened 1 year ago

sgrannem commented 1 year ago

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 If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

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

300GB of disk space still available.

fkaiserbio commented 1 year ago

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?