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Refinement of macromolecular structures by the maximum-likelihood method.
This paper reviews the mathematical basis of maximum likelihood. The likelihood function for macromolecular structures is extended to include prior phase information and experimental standardExpand
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Overview of the CCP4 suite and current developments
An overview of the CCP4 software suite for macromolecular crystallography is given.
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REFMAC5 for the refinement of macromolecular crystal structures
The general principles behind the macromolecular crystal structure refinement program REFMAC5 are described.
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How good are my data and what is the resolution?
The new scaling program AIMLESS is described and tests of refinements at different resolutions are compared with analyses from the scaling step.
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Use of TLS parameters to model anisotropic displacements in macromolecular refinement.
An essential step in macromolecular refinement is the selection of model parameters which give as good a description of the experimental data as possible while retaining a realistic data-to-parameterExpand
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REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use.
One of the most important aspects of macromolecular structure refinement is the use of prior chemical knowledge. Bond lengths, bond angles and other chemical properties are used in restrainedExpand
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Efficient anisotropic refinement of macromolecular structures using FFT.
This paper gives the equations for the use of fast Fourier transformations in individual atomic anisotropic refinement. Restraints on bonded atoms, on the sphericity of each atom and betweenExpand
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BALBES: a molecular-replacement pipeline
The fully automated pipeline, BALBES, integrates a redesigned hierarchical database of protein structures with their domains and multimeric organization, and solves molecular-replacement problemsExpand
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Macromolecular TLS refinement in REFMAC at moderate resolutions.
Publisher Summary This chapter discusses the translation, rotation, and screw-rotation (TLS) parameterization of anisotropic displacement parameters (ADPs). In general, each atom can deviateExpand
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High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy☆
Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of theExpand
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