Abstract: Disclosed are high-throughput methods for determining crystal structures from X-ray diffraction data, for example high-throughput crystal structure determination methods employing flexible, high-throughput modular computational pipelines, such as Bioperl computational pipelines. High-throughput methods for determining crystal structures can be fully or partially automated, and can be fully or partially computer executed. Crystal structure determination methods employing a pipeline interface, work flow manager and/or output parsers can be used to optimize the amount of structural information derived from an X-ray diffraction data set and increase the efficiency of calculating crystal structures from X-ray diffraction data.