How are metals taken into consideration in Homology?
The metal ions are removed during the simulation but we add constraints to the backbone of the templates that helps to preserve the open/close conformations. Once we implement template selection you will be able to select the templates that matches the conformation you are interested in. We do plan to add full metal support to the pipeline. The way we envision this is by letting you select the metal ions from one of the templates that you want to go into the simulation.