Acta Crystallographica Section D Structural Biology· 2018Q1
Real-space refinement in <i>PHENIX</i> for cryo-EM and crystallography
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- Q1SCImago
- 2018year
Short summary
The PHENIX suite now includes phenix.real_space_refine, a program that rapidly refines atomic models against low-resolution cryo-EM and crystallographic data using a simplified target function and incorporating diverse restraints.
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Key points
- PHENIX now offers phenix.real_space_refine for rapid atomic model refinement.
- A simplified target function enables fast calculations and optimal data-restraint weight identification.
- The program incorporates diverse restraints: covalent geometry, secondary structure, rotamers, and molecular symmetry.
- Refinement against low-resolution data (≤ 6 Å) shows significant model improvement and better map fitting.
AI-generated from the title and abstract; the full text is not read.
Abstract
This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
The authors' abstract, as published at the source. Acta Crystallographica Section D Structural Biology, 2018 · DOI ↗
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Field: Materials Chemistry
Materials ChemistryMaterials Science