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Using the ligand overlay functionality in Hermes 2023.1 or 2023.2 on Linux fails with an error about reading the initialisation file


Hermes 2023.1 or 2023.2 may fail to run the ligand overlay tool with the following error:

MoleculeGeometryPreferences: there was a problem initialising Mogul: errors=Problem reading initialisation file

This issue is resolved in the 2023.3 release.


To enable this to work with 2023.1 or 2023.2 releases, a workaround is to set CCDC_MOGUL_INITIALISATION_FILE to the mogul.ini file in your Hermes installation, e.g.

export CCDC_MOGUL_INITIALISATION_FILE=/home/user/CCDC/ccdc-software/hermes/bin/mogul.ini

before starting Hermes.