Native ion channels play key roles in biological systems, and engineered versions are widely used as chemogenetic tools and in sensing devices 1,2 . Protein design has been harnessed to generate pore-containing transmembrane proteins, but the capability to design ion selectivity based on the interactions between ions and selectivity filter residues, a crucial feature of native ion channels 3 , has been constrained by the lack of methods to place the metal-coordinating residues with atomic-level precision. Here we describe a bottom-up RFdiffusion-based approach to construct Ca 2+ channels from defined selectivity filter residue geometries, and use this approach to design symmetric oligomeric channels with Ca 2+ selectivity filters having different coordination numbers and different geometries at the entrance of a wide pore buttressed by multiple transmembrane helices. The designed channel proteins assemble into homogenous pore-containing particles, and for both tetrameric and hexameric ion-coordinating configurations, patch-clamp experiments show that the designed channels have higher conductances for Ca 2+ than for Na + and other divalent ions (Sr 2+ and Mg 2+ ). Cryo-electron microscopy indicates that the design method has high accuracy: the structure of the hexameric Ca 2+ channel is nearly identical to the design model. Our bottom-up design approach now enables the testing of hypotheses relating filter geometry to ion selectivity by direct construction, and provides a roadmap for creating selective ion channels for a wide range of applications.