Membrane vs Transmembrane

[alexandrefassio]

Membrane vs Transmembrane

[JorgeRoel]

Hi @alexandrefassio

Thanks for your query. This is indeed the expected behaviour in LightDock. While --transmembrane was meant to sample transmembrane regions i.e. those between upper and lower regions and therefore model dimerization processes (not systematically tested though), --membrane was conceived to model membrane protein-soluble interactions (either extracellular or cytosolic). The generation of the swarms is driven by the orientation of the input system (protein + membrane) in LightDock. If you want to sample "lower" regions, you would only need to apply a 180º transformation across your desired axis.

To sample both regions, you might need to either perform to independent runs or perform two different setups and then combined the files in a appropriate manner (avoiding duplicates in file names) and possibly manually modifying the setup.json.