Low-resolution refinement tools in REFMAC5

By R. Nicholls, F. Long, G. Murshudov. 2012

220 citations recorded by the source corpus.

Low-resolution refinement tools implemented in REFMAC5 are described, including the use of external structural restraints, helical restraints and regularized anisotropic map sharpening.

Subfields: Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Paul D. Adams
2. Pavel V. Afonine
3. T. C. Terwilliger
4. Nigel W. Moriarty
5. Nathaniel Echols
6. O. Sobolev
7. Randy J. Read
8. G. Murshudov

In Molecular Biology

1. Paul D. Adams
2. Pavel V. Afonine
3. T. C. Terwilliger
4. Nigel W. Moriarty
5. O. Sobolev
6. Nathaniel Echols
7. Randy J. Read
8. G. Murshudov

Citations in the corpus

• Automated map sharpening by maximization of detail and connectivity (2018, methodology): “Nicholls et al. (2012) develop procedures for optimizing anisotropic versions of displacement factors based on considering sharpening as an inverse deblurring problem.”
• Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data (2019, methodology): “Traditionally, this has been performed in programs such as REFMAC or RELION.12,13 More sophisticated ways of improving the map are now available such as LocScale or confidence maps that provide an alternative interpretation.14,15 In Coot, one can generate sharpened and blurred maps using different t”
• AceDRG: a stereochemical description generator for ligands (2017, background): “…by prior knowledge pertaining ISSN 2059-7983 to the chemistry and structure of the molecules under study in order to address the problem of missing high-resolution information (Murshudov et al. , 2011; Nicholls et al. , 2012; Schro¨der et al. , 2010; Adams et al. , 2010; Smart et al. , 2012).”
• Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM (2018, methodology): “Specifically, we focus on the program REFMAC5 (Murshudov et al., 2011), noting that other refinement software and suites employ similar technologies (see, for example, Afonine et al., 2013).”
• Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement (2014, result): “%) or REFMAC5 (average of 2.64%).”
• Recent developments in the CCP-EM software suite (2017, methodology): “A Wilson plot is displayed, allowing inspection of potential truncation pathologies arising from over-sharpening (Nicholls et al., 2012), and the task is linked to Coot for visual inspection.”
• Structural basis for RNA translocation by DEAH-box ATPases (2019, methodology): “The ctPrp22-Apo structure was additionally refined with external restraints using the ctPrp22 model from the RNA complex as a reference structure (42).”