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. Author manuscript; available in PMC: 2012 Sep 1.

Published in final edited form as: Methods. 2011 Jul 29;55(1):94–106. doi: 10.1016/j.ymeth.2011.07.005

Automated molecular replacement with the AutoMR wizard in Phenix. A) The AutoMR wizard has a simple and an advanced interface. The simple interface is designed for cases where there is only one molecular component in the asymmetric unit (ASU) – multiple copies of that component are supported. The advanced interface is provided for more complex cases with multiple components. In this example there are two components that form a complex in the ASU. It is necessary to define the search model(s), which will be placed in the crystal, and the contents of the ASU (shown in the inset). The latter is best achieved by providing sequence files, as these can then also be used for automated model building subsequent to the molecular replacement. B) During the run new tabs are generated to show the progress of the molecular replacement. At the end of the run the Summary tab provides a list of the files generated, links for easy viewing of the model and current electron density map in Coot or PyMOL, and links to running the next step in Phenix: automated model (re)building with the AutoBuild wizard, structure refinement with phenix.refine, or combined MR-SAD phasing in Phaser.

Automated molecular replacement with the AutoMR wizard in Phenix. A) The AutoMR wizard has a simple and an advanced interface. The simple interface is designed for cases where there is only one molecular component in the asymmetric unit (ASU) – multiple copies of that component are supported. The advanced interface is provided for more complex cases with multiple components. In this example there are two components that form a complex in the ASU. It is necessary to define the search model(s), which will be placed in the crystal, and the contents of the ASU (shown in the inset). The latter is best achieved by providing sequence files, as these can then also be used for automated model building subsequent to the molecular replacement. B) During the run new tabs are generated to show the progress of the molecular replacement. At the end of the run the Summary tab provides a list of the files generated, links for easy viewing of the model and current electron density map in Coot or PyMOL, and links to running the next step in Phenix: automated model (re)building with the AutoBuild wizard, structure refinement with phenix.refine, or combined MR-SAD phasing in Phaser.