Comparison of automated crystallographic model-building pipelines

A comparison of four protein model-building pipelines (ARP/wARP, Buccaneer, PHENIX AutoBuild and SHELXE) was performed using data sets from 202 experimentally phased cases, both with the data as observed and truncated to simulate lower resolutions. All pipelines were run using default parameters. Additionally, an ARP/wARP run was completed using models from Buccaneer. All pipelines achieved nearly complete protein structures and low R work/R free at resolutions between 1.2 and 1.9 Å, with PHENIX AutoBuild and ARP/wARP producing slightly lower R factors. At lower resolutions, Buccaneer leads to significantly more complete models.