Florian Kaiser

Could you please give more details? Ideally the PDB file you used and the exact specification of the bond you are expecting PLIP to detect.

Thanks for pointing this out and your detailed investigation! Might be even something to include as a command line option for advanced users.

Hi @dangthatsright currently, PLIP does not support passing in multiple ligands as SDF. Maybe it could be also an Idea to put all the poses into a single PDB file...

JSON support is already under consideration and will be added in the next release. See branch `feature/json` for a stub.

Thanks for the report! This issue is caused by OpenBabel that PLIP is using to decide between acceptor and donor atoms for hydrogen bonds. OpenBabel does not recognize the backbone...

Hi Jaime, thanks for your elaborate reply and the very helpful resources. This will be definitely helpful to improve H-bond detection for PLIP. Briefly, PLIP does the following: - protonate...

I can't reproduce this. Both commands generate visualizations as expected when running with Docker. Please check your PyMol installation and whether Python bindings are correctly linked. ``` $ docker run...

This is very strange. Does PLIP output debug log records? You are using the `-v` flag, so it should. Could you please paste a full log output here? Also it...

Thanks for the very detailed report. We will investigate this further and reopen the issue.

Hi there! Currently, this is not officially supported by PLIP. We already discussed this and came to the conclusion that a proper parameterization would be needed to obtain valid results....