We first show that the training protocol described in the Methods is effective and produces an accurate model for predicting DNA electron densities. Specifically, we test if a machine learning model trained only on base pair steps can make accurate predictions for arbitrary DNA structures. We evaluate the fit of the model by directly comparing to a test set of electron densities calculated from ab initio quantum calculations. Since quantum calculations are restricted by system size, the test set was limited to DNA structures with sequence lengths ranging from two to five base pairs.