ModelCraft: an advanced automated model-building pipeline using Buccaneer - Paul Bond
Buccaneer is an automated protein model-building program suited for use across a range of resolutions. It is iterated in a pipeline along with global refinement using REFMAC5 to produce an updated model and map, which are then passed back to Buccaneer. Tests of our existing pipeline on a large set of molecular-replacement structures, including some with poor models and partial solutions, showed worse performance than expected where many structures could not be completed.
We created a new pipeline called ModelCraft that replaces the previous pipeline to include nucleic acid building using Nautilus, classical density modification using Parrot, phase improvement through the addition of dummy atoms, model pruning and side-chain rebuilding using Coot, as well as other pipeline improvements such as automatic stopping and default selection of the best model. ModelCraft dramatically improves results for molecular-replacement structures at all resolutions.