, Volume 13, Issue 2, pp 81-90,
Open Access This content is freely available online to anyone, anywhere at any time.
Date: 15 Mar 2012

phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta

Abstract

The combination of algorithms from the structure-modeling field with those of crystallographic structure determination can broaden the range of templates that are useful for structure determination by the method of molecular replacement. Automated tools in phenix.mr_rosetta simplify the application of these combined approaches by integrating Phenix crystallographic algorithms and Rosetta structure-modeling algorithms and by systematically generating and evaluating models with a combination of these methods. The phenix.mr_rosetta algorithms can be used to automatically determine challenging structures. The approaches used in phenix.mr_rosetta are described along with examples that show roles that structure-modeling can play in molecular replacement.

The phenix.mr_rosetta tools and instructions for their use are available as part of Phenix (www.phenix-online.org). The Rosetta software is available from http://depts.washington.edu/uwc4c/express-licenses/assets/rosetta/. A local installation containing both Phenix and Rosetta is necessary to run phenix.mr_rosetta. Sample scripts for running phenix.mr_rosetta, test data, and some of the data and scripts used in this work are all available at http://www.phenix-online.org/phenix_data/terwilliger/rosetta_2011/.