MRC2020: improvements to Ximdisp and the MRC image-processing programs.

The great success of single-particle electron cryo-microscopy (cryoEM) during the last decade has involved the development of powerful new computer programs and packages that guide the user along a recommended processing workflow, in which the wisdom and choices made by the developers help everyone, especially new users, to obtain excellent results. The ability to carry out novel, non-standard or unusual combinations of image-processing steps is sometimes compromised by the convenience of a standard procedure. Some of the older programs were written with great flexibility and are still very valuable. Among these, the original MRC image-processing programs for structure determination by 2D crystal and helical processing alongside general-purpose utility programs such as Ximdisp, label, imedit and twofile are still available. This work describes an updated version of the MRC software package (MRC2020) that is freely available from CCP-EM. It includes new features and improvements such as extensions to the MRC format that retain the versatility of the package and make it particularly useful for testing novel computational procedures in cryoEM.

The new CCP4 Coordinate Library as a toolkit for the design of coordinate-related applications in protein crystallography.

The new CCP4 Coordinate Library is a development aiming to provide a common layer of coordinate-related functionality to the existing applications in the CCP4 suite, as well as a variety of tools that can simplify the design of new applications where they relate to atomic coordinates. The Library comprises a wide spectrum of useful functions, ranging from parsing coordinate formats and elementary editing operations on the coordinate hierarchy of biomolecules, to high-level functionality such as calculation of secondary structure, interatomic bonds, atomic contacts, symmetry transformations, structure superposition and many others. Most of the functions are available in a C++ object interface; however, a Fortran interface is provided for compatibility with older CCP4 applications. The paper describes the general principles of the Library design and the most important functionality. The Library, together with documentation, is available under the LGPL license from the CCP4 suite version 5.0 and higher.

An overview of the CCP4 project in protein crystallography: an example of a collaborative project.

The Collaborative Computational Project Number 4 (CCP4) was established in 1979 to promote collaboration between UK groups writing software for protein crystallography. CCP4 now distributes a large software suite and is active in developing new software. Equally importantly, CCP4 provides a focus for the whole protein crystallography community via meetings, workshops, email lists and various publications. In this Article, an overview is given of CCP4 activities and their administration. The emphasis is on generic features of the collaboration rather than details specific to protein crystallography. The CCP4 model has inspired similar developments in NMR, and it is hoped that the biological XAS community may pursue similar collaboration.

Ongoing developments in CCP4 for high-throughput structure determination.

Collaborative Computational Project Number 4 (CCP4) was established in 1979 to promote collaboration between UK groups writing software for protein crystallography. From these beginnings, CCP4 now distributes a large software suite and is active in developing new software. In this article, an overview is given of recent and ongoing developments in the CCP4 software suite, in particular as they pertain to high-throughput studies. Developments in individual programs are discussed first, although these are covered in more detail elsewhere. The bulk of the article focuses on the infrastructure of the software suite which allows the user to move effortlessly between different programs or to create automated schemas. Major changes to the software library at the heart of the CCP4 suite, developments in the CCP4 graphical user interface, and data management within CCP4 are discussed. The latter is crucial to high-throughput studies, where a large number of data are imported, created and finally archived.

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-parameter ratio. This is particularly true of the choice of atomic displacement parameters, where the move from individual isotropic to individual anisotropic refinement involves a sixfold increase in the number of required displacement parameters. The number of refinement parameters can be reduced by using collective variables rather than independent atomic variables and one of the simplest examples of this is the TLS parameterization for describing the translation, libration and screw-rotation displacements of a pseudo-rigid body. This article describes the implementation of the TLS parameterization in the macromolecular refinement program REFMAC. Derivatives of the residual with respect to the TLS parameters are expanded in terms of the derivatives with respect to individual anisotropic U values, which in turn are calculated using a fast Fourier transform technique. TLS refinement is therefore fast and can be used routinely. Examples of TLS refinement are given for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a transcription activator GerE, for both of which there is data to only 2.0 A, so that individual anisotropic refinement is not feasible. GAPDH has been refined with between one and four TLS groups in the asymmetric unit and GerE with six TLS groups. In both cases, inclusion of TLS parameters gives improved refinement statistics and in particular an improvement in R and free R values of several percent. Furthermore, GAPDH and GerE have two and six molecules in the asymmetric unit, respectively, and in each case the displacement parameters differ significantly between molecules. These differences are well accounted for by the TLS parameterization, leaving residual local displacements which are very similar between molecules and to which NCS restraints can be applied.