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. 2023 Jun 1;79(Pt 6):449-461.
doi: 10.1107/S2059798323003595. Epub 2023 May 30.

The CCP4 suite: integrative software for macromolecular crystallography

Jon Agirre  1 , Mihaela Atanasova  1 , Haroldas Bagdonas  1 , Charles B Ballard  2 , Arnaud Baslé  3 , James Beilsten-Edmands  4 , Rafael J Borges  5 , David G Brown  6 , J Javier Burgos-Mármol  7 , John M Berrisford  8 , Paul S Bond  1 , Iracema Caballero  9 , Lucrezia Catapano  10 , Grzegorz Chojnowski  11 , Atlanta G Cook  12 , Kevin D Cowtan  1 , Tristan I Croll  13 , Judit É Debreczeni  14 , Nicholas E Devenish  4 , Eleanor J Dodson  1 , Tarik R Drevon  2 , Paul Emsley  10 , Gwyndaf Evans  4 , Phil R Evans  10 , Maria Fando  2 , James Foadi  15 , Luis Fuentes-Montero  4 , Elspeth F Garman  16 , Markus Gerstel  4 , Richard J Gildea  4 , Kaushik Hatti  13 , Maarten L Hekkelman  17 , Philipp Heuser  18 , Soon Wen Hoh  1 , Michael A Hough  4 , Huw T Jenkins  1 , Elisabet Jiménez  9 , Robbie P Joosten  17 , Ronan M Keegan  2 , Nicholas Keep  19 , Eugene B Krissinel  2 , Petr Kolenko  20 , Oleg Kovalevskiy  2 , Victor S Lamzin  11 , David M Lawson  21 , Andrey A Lebedev  2 , Andrew G W Leslie  10 , Bernhard Lohkamp  22 , Fei Long  10 , Martin Malý  23 , Airlie J McCoy  13 , Stuart J McNicholas  1 , Ana Medina  9 , Claudia Millán  13 , James W Murray  24 , Garib N Murshudov  10 , Robert A Nicholls  10 , Martin E M Noble  25 , Robert Oeffner  13 , Navraj S Pannu  26 , James M Parkhurst  4 , Nicholas Pearce  27 , Joana Pereira  28 , Anastassis Perrakis  17 , Harold R Powell  24 , Randy J Read  13 , Daniel J Rigden  7 , William Rochira  1 , Massimo Sammito  29 , Filomeno Sánchez Rodríguez  1 , George M Sheldrick  30 , Kathryn L Shelley  31 , Felix Simkovic  7 , Adam J Simpkin  6 , Pavol Skubak  26 , Egor Sobolev  18 , Roberto A Steiner  32 , Kyle Stevenson  2 , Ivo Tews  23 , Jens M H Thomas  7 , Andrea Thorn  33 , Josep Triviño Valls  9 , Ville Uski  2 , Isabel Usón  9 , Alexei Vagin  1 , Sameer Velankar  8 , Melanie Vollmar  8 , Helen Walden  34 , David Waterman  2 , Keith S Wilson  1 , Martyn D Winn  35 , Graeme Winter  4 , Marcin Wojdyr  36 , Keitaro Yamashita  10
Affiliations

The CCP4 suite: integrative software for macromolecular crystallography

Jon Agirre et al. Acta Crystallogr D Struct Biol. .

Abstract

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.

Keywords: CCP4; Collaborative Computational Project No. 4; crystallography software; macromolecular crystallography.

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Figures

Figure 1
Figure 1
Evolution in the size of the CCP4 suite from version 4.2 (2002) through to version 8.0 (2022). Some representative programs included in the releases are highlighted in orange. The update mechanism (CCP4-um) was first used in version 6.3. New graphical interfaces were introduced in versions 7.0 (CCP4i2) and 7.1 (CCP4 Cloud). Coot and CCP4mg were originally distributed separately, but were bundled with the suite from version 6.5. For reference, the sizes of two popular contemporary storage devices are shown as dotted lines; please note that these were never targeted as distribution media.
Figure 2
Figure 2
Comparison of the new CCP4 graphical user interface offerings: (a) desktop (CCP4i2) and (b) online (CCP4 Cloud). The same pipeline (Crank-2) has been run on both interfaces. The reports show equivalent graphs due to the use of a compatibility layer that allows the same report code to run on both platforms.
Figure 3
Figure 3
A collection of newer representations included in the CCP4 Molecular Graphics project (CCP4mg). (a) PDB entry 2bn3 is a high-resolution model of insulin (Nanao et al., 2005 ▸); it is shown here as worms, with water molecules drawn as ellipsoids, both coloured and scaled by the anisotropic B factors of the model. (b) PDB entry 3v8x (Noinaj et al., 2012 ▸) is a structure of human transferrin (chain B), drawn here as a solvent-accessible surface with N-glycans shown as Glycoblocks (McNicholas & Agirre, 2017 ▸). (c) PDB entry 3c02, a structure of aquaglyceroporin from Plasmodium falciparum (Newby et al., 2008 ▸), embedded in a lipid bilayer by CHARMM-GUI (Jo et al., 2008 ▸); lipids are shown as cartoons.
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