RosettaCommons / RosettaCommons/foundry

Missing ligand at zero occupancy

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#271 0 comments 0 reactions 1 assignee View on GitHub

@rclune is already working on this.

Since Apr 20, 2026.

bug
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Python
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Description

Hey all, this is not a critical bug, but unexpected behavior that might save others some time if documented. When fetching and saving ligands from the RCSB in PyMol (fetch CCD), the ligands are stored with zero occupancy. Ligands with zero occupancy seem to be ignored by RFdiffusion3 (they do not appear in the generated outputs .cif files. Haven't checked what happens within RFD3 internally). This behavior might be worth at least a warning in the logs?

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