Marcin Wojdyr

CCP4i2: the new graphical user interface to the CCP4 program suite

CCP4i2 is a graphical user interface to the CCP4 (Collaborative Computational Project, Number 4) software suite and a Python language framework for software automation.

A pipeline for the rapid generation of difference maps from protein crystals

In 2013 MX beamlines at the Diamond synchrotron deployed an automated software pipeline, called DIMPLE, for rapid processing of crystals that contain a known protein and possibly a ligand bound. DIMPLE takes the already known apo structure for the target protein, compares it with the electron density map from X-ray diffraction images, and visualizes areas of the electron density unaccounted for by the structure model. When processing batches of crystals, such feedback allows the user to better decide what to measure next which leads to a more efficient use of the beam time. This year weve enhanced the pipeline to cover more complex cases, including changes in the space group and some changes in conformation. With multiple molecular replacement computations run in parallel, the time from shooting to viewing the difference map is still only a few minutes. While the software is developed primarily for use at synchrotron beamlines, it is included in the CCP4 suite and can be used as well for in-house automation.

SIMBAD: a sequence-independent molecular-replacement pipeline

SIMBAD is a sequence-independent molecular-replacement pipeline for solving difficult molecular-replacement cases where contaminants have been crystallized. It can also be used to find structurally related search models where no obvious homologue can be found through sequence-based searching.

Gemmi – new GΦL+CCP4 project for handling (mm)CIF files

In the first year of the development we focus on handling mmCIF files and monomer library files (ligand CIFs). We started from the lowest level parsing CIF files and validating them with DDL dictionaries. Next, we will provide interface to manipulate the structure in terms of models, chains, residues and atoms. On top of it we will provide a collection of algorithms, primarily for use in macromolecular refinement programs. Finally, the library will be integrated with BUSTER and Refmac.

CCP4: a resource for macromolecular crystallography

CCP4 has been serving the software needs of the protein crystallography community for more than 30 years. In this time the CCP4 Suite of software has been refined through contributions from some of the leading developers in the field of protein crystallographic software and the feedback of both expert and novice users. Today it is a highly comprehensive suite, providing tools and packages covering all aspects from data collection through to structure deposition. Here we will present details of the latest release series of the Suite, version 6.4. This release brings updates to many of the key elements in the Suite. The most obvious of these is the integration of the rolling updates mechanism. This is used to distribute timely fixes, update existing programs and introduce new functionality to users of the suite. Recent updates have seen updates to major programs such as phaser and imosflm/mosflm, and the introduction of a major overhaul of the Experimental Phasing pipeline Crank. An overview is given of the operation behind the updates and releases, including the jhbuild system, repositories and testing, the availability of nightly builds, and work towards the next major release of CCP4. This will see the integration of the CCP4MG package, along with preparations for the introduction of the long awaited CCP4i2.