Automating tasks in protein structure determination with the clipper python module

The CCP4 suite: integrative software for macromolecular crystallography

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.

Iris: Interactive all-in-one graphical validation of 3D protein model iterations

Iris validation is a Python package created to represent comprehensive per‐residue validation metrics for entire protein chains in a compact, readable and interactive view. These metrics can either be calculated by Iris, or by a third‐party program such as MolProbity. We show that those parts of a protein model requiring attention may generate ripples across the metrics on the diagram, immediately catching the modeler's attention. Iris can run as a standalone tool, or be plugged into existing structural biology software to display per‐chain model quality at a glance, with a particular emphasis on evaluating incremental changes resulting from the iterative nature of model building and refinement. Finally, the integration of Iris into the CCP4i2 graphical user interface is provided as a showcase of its pluggable design.

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps. ISOLDE combines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualized in real time. Using the recently described 3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated how ISOLDE can be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model.

Fragon: rapid high-resolution structure determination from ideal protein fragments

Correctly positioning ideal protein fragments by molecular replacement presents an attractive method for obtaining preliminary phases when no template structure for molecular replacement is available. This has been exploited in several existing pipelines. This paper presents a new pipeline, named Fragon, in which fragments (ideal α-helices or β-strands) are placed using Phaser and the phases calculated from these coordinates are then improved by the density-modification methods provided by ACORN. The reliable scoring algorithm provided by ACORN identifies success. In these cases, the resulting phases are usually of sufficient quality to enable automated model building of the entire structure. Fragon was evaluated against two test sets comprising mixed α/β folds and all-β folds at resolutions between 1.0 and 1.7 Å. Success rates of 61% for the mixed α/β test set and 30% for the all-β test set were achieved. In almost 70% of successful runs, fragment placement and density modification took less than 30 min on relatively modest four-core desktop computers. In all successful runs the best set of phases enabled automated model building with ARP/wARP to complete the structure.

Forty years of collaborative computational crystallography

A brief overview is provided of the history of collaborative computational crystallography, with an emphasis on the Collaborative Computational Project No. 4. The key steps in its development are outlined, with consideration also given to the underlying reasons which contributed, and ultimately led to, the unprecedented success of this venture.