These scripts demonstrate the use of IMP, MODELLER, FoXS, and AllosMod, and Minimal Ensemble Search in the modeling of the Nup133 protein in the S. cerevisiae Nuclear Pore Complex (NPC). First, MODELLER is used to generate an initial comparative model of Nup133 guided by FoXS fits to SAXS data. Then, the model was subjected to conformational sampling with AllosMod, and finally Minimal Ensemble Search was used to identify four models that together reproduced both the SAXS data and a set of electron microscopy class averages. The final model was also validated against a set of chemical cross-links, that were not used in the modeling. For more information about how to reproduce this modeling, see the Sali lab website or the README file.