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.

Biological Sciences Institute for Life Sciences University of Southampton Southampton SO17 1BJ United Kingdom

Biosciences Institute Newcastle University Newcastle upon Tyne NE2 4HH United Kingdom

Biozentrum and SIB Swiss Institute of Bioinformatics University of Basel 4056 Basel Switzerland

Crystallographic Methods Institute of Molecular Biology of Barcelona Barcelona Science Park Helix Building Baldiri Reixac 15 08028 Barcelona Spain

Department of Biochemistry and Metabolism John Innes Centre Norwich NR4 7UH United Kingdom

Department of Biochemistry University of Oxford Dorothy Crowfoot Hodgkin Building Oxford OX1 3QU United Kingdom

Department of Biological Sciences Institute of Structural and Molecular Biology Birkbeck College London WC1E 7HX United Kingdom

Department of Haematology Cambridge Institute for Medical Research University of Cambridge Hills Road Cambridge CB2 0XY United Kingdom

Department of Infectious Diseases Leiden University Medical Center PO Box 9600 2300 RC Leiden The Netherlands

Department of Life Sciences Imperial College London South Kensington Campus London SW7 2AZ United Kingdom

Department of Mathematical Sciences University of Bath Bath United Kingdom

Department of Medical Biochemistry and Biophysics Karolinska Institutet SE 171 77 Stockholm Sweden

Department of Physics Chemistry and Biology Linköping University SE 581 83 Linköping Sweden

Department of Structural Chemistry Georg August Universität Göttingen Tammannstrasse 4 37077 Göttingen Germany

Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0DE United Kingdom

Discovery Centre Biologics Engineering AstraZeneca Biomedical Campus 1 Francis Crick Avenue Trumpington Cambridge CB2 0AA United Kingdom

Discovery Sciences R and D BioPharmaceuticals AstraZeneca Darwin Building Cambridge Science Park Milton Road Cambridge CB4 0WG United Kingdom

European Molecular Biology Laboratory c o DESY Notkestrasse 85 22607 Hamburg Germany

European Molecular Biology Laboratory Hamburg Unit Notkestrasse 85 22607 Hamburg Germany

Faculty of Nuclear Sciences and Physical Engineering Czech Technical University Prague Břehová 7 115 19 Prague 1 Czech Republic

Global Phasing Limited Sheraton House Castle Park Cambridge CB3 0AX United Kingdom

Institute for Nanostructure and Solid State Physics Universität Hamburg 22761 Hamburg Germany

Institute for Protein Design University of Washington Seattle WA 98195 USA

Institute of Systems Molecular and Integrative Biology University of Liverpool Liverpool L69 7ZB United Kingdom

Laboratoires Servier SAS Institut de Recherches Croissy sur Seine France

MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH United Kingdom

Oncode Institute and Department of Biochemistry Netherlands Cancer Institute Amsterdam The Netherlands

Protein Data Bank in Europe European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

Randall Centre for Cell and Molecular Biophysics Faculty of Life Sciences and Medicine King's College London London SE1 9RT United Kingdom

School of Molecular Biosciences College of Medical Veterinary and Life Sciences University of Glasgow Glasgow United Kingdom

Scientific Computing Department Science and Technology Facilities Council Didcot OX11 0FA United Kingdom

STFC Rutherford Appleton Laboratory Didcot OX11 0FA United Kingdom

The Center of Medicinal Chemistry Av Dr André Tosello 550 13083 886 Campinas Brazil

The Wellcome Centre for Cell Biology University of Edinburgh Michael Swann Building Max Born Crescent The King's Buildings Edinburgh EH9 3BF United Kingdom

Translational and Clinical Research Institute Newcastle University Paul O'Gorman Building Medical School Framlington Place Newcastle upon Tyne NE2 4HH United Kingdom

York Structural Biology Laboratory Department of Chemistry University of York York YO10 5DD United Kingdom

Zobrazit více v PubMed

Agirre, J. & Dodson, E. (2018). PubMed PMC

Agirre, J., Iglesias-Fernández, J., Rovira, C., Davies, G. J., Wilson, K. S. & Cowtan, K. D. (2015). PubMed

Allen, F. H. & Bruno, I. J. (2010). PubMed

Armstrong, D. R., Berrisford, J. M., Conroy, M. J., Gutmanas, A., Anyango, S., Choudhary, P., Clark, A. R., Dana, J. M., Deshpande, M., Dunlop, R., Gane, P., Gáborová, R., Gupta, D., Haslam, P., Koča, J., Mak, L., Mir, S., Mukhopadhyay, A., Nadzirin, N., Nair, S., Paysan-Lafosse, T., Pravda, L., Sehnal, D., Salih, O., Smart, O., Tolchard, J., Varadi, M., Svobodova-Vařeková, R., Zaki, H., Kleywegt, G. J. & Velankar, S. (2020). PubMed PMC

Atanasova, M., Nicholls, R. A., Joosten, R. P. & Agirre, J. (2022). PubMed PMC

Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., Millán, C., Park, H., Adams, C., Glassman, C. R., DeGiovanni, A., Pereira, J. H., Rodrigues, A. V., van Dijk, A. A., Ebrecht, A. C., Opperman, D. J., Sagmeister, T., Buhlheller, C., Pavkov-Keller, T., Rathina­swamy, M. K., Dalwadi, U., Yip, C. K., Burke, J. E., Garcia, K. C., Grishin, N. V., Adams, P. D., Read, R. J. & Baker, D. (2021).

Bagdonas, H., Fogarty, C. A., Fadda, E. & Agirre, J. (2021). PubMed

Bagdonas, H., Ungar, D. & Agirre, J. (2020). PubMed PMC

Beilsten-Edmands, J., Winter, G., Gildea, R., Parkhurst, J., Waterman, D. & Evans, G. (2020). PubMed PMC

Bibby, J., Keegan, R. M., Mayans, O., Winn, M. D. & Rigden, D. J. (2012). PubMed

Bond, P. S. & Cowtan, K. D. (2022). PubMed PMC

Brewster, A. S., Waterman, D. G., Parkhurst, J. M., Gildea, R. J., Young, I. D., O’Riordan, L. J., Yano, J., Winter, G., Evans, G. & Sauter, N. K. (2018). PubMed PMC

Brown, A., Long, F., Nicholls, R. A., Toots, J., Emsley, P. & Murshudov, G. (2015). PubMed PMC

Burnley, T., Palmer, C. M. & Winn, M. (2017). PubMed PMC

Caballero, I., Sammito, M., Millán, C., Lebedev, A., Soler, N. & Usón, I. (2018). PubMed PMC

Casañal, A., Lohkamp, B. & Emsley, P. (2020). PubMed PMC

Catapano, L., Steiner, R. A. & Murshudov, G. N. (2021).

Chojnowski, G., Simpkin, A. J., Leonardo, D. A., Seifert-Davila, W., Vivas-Ruiz, D. E., Keegan, R. M. & Rigden, D. J. (2022). PubMed PMC

Chojnowski, G., Sobolev, E., Heuser, P. & Lamzin, V. S. (2021). PubMed PMC

Clabbers, M. T. B., Gruene, T., Parkhurst, J. M., Abrahams, J. P. & Waterman, D. G. (2018). PubMed PMC

Cowtan, K. (2006). PubMed

Cowtan, K. (2010). PubMed PMC

Cowtan, K. (2014). PubMed PMC

Cowtan, K. & Agirre, J. (2018). PubMed PMC

Cowtan, K., Metcalfe, S. & Bond, P. (2020). PubMed PMC

Dialpuri, J. S., Bagdonas, H., Atanasova, M., Schofield, L. C., Hekkelman, M. L., Joosten, R. P. & Agirre, J. (2023). PubMed PMC

Eddy, S. R. (2011). PubMed PMC

Emsley, P. (2017). PubMed PMC

Emsley, P. & Cowtan, K. (2004). PubMed

Emsley, P. & Crispin, M. (2018). PubMed PMC

Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). PubMed PMC

Evans, P. R. & Murshudov, G. N. (2013). PubMed PMC

French, S. & Wilson, K. (1978).

Fuentes-Montero, L., Parkhurst, J., Gerstel, M., Gildea, R., Winter, G., Vollmar, M., Waterman, D. & Evans, G. (2016).

Gildea, R. J., Beilsten-Edmands, J., Axford, D., Horrell, S., Aller, P., Sandy, J., Sanchez-Weatherby, J., Owen, C. D., Lukacik, P., Strain-Damerell, C., Owen, R. L., Walsh, M. A. & Winter, G. (2022). PubMed PMC

Ginn, H. M., Brewster, A. S., Hattne, J., Evans, G., Wagner, A., Grimes, J. M., Sauter, N. K., Sutton, G. & Stuart, D. I. (2015). PubMed PMC

Gore, S., Sanz García, E., Hendrickx, P. M. S., Gutmanas, A., Westbrook, J. D., Yang, H., Feng, Z., Baskaran, K., Berrisford, J. M., Hudson, B. P., Ikegawa, Y., Kobayashi, N., Lawson, C. L., Mading, S., Mak, L., Mukhopadhyay, A., Oldfield, T. J., Patwardhan, A., Peisach, E., Sahni, G., Sekharan, M. R., Sen, S., Shao, C., Smart, O. S., Ulrich, E. L., Yamashita, R., Quesada, M., Young, J. Y., Nakamura, H., Markley, J. L., Berman, H. M., Burley, S. K., Velankar, S. & Kleywegt, G. J. (2017).

Gore, S., Velankar, S. & Kleywegt, G. J. (2012). PubMed PMC

Grosse-Kunstleve, R. W., Sauter, N. K., Moriarty, N. W. & Adams, P. D. (2002).

Jenkins, H. T. (2018). PubMed PMC

Jo, S., Kim, T., Iyer, V. G. & Im, W. (2008). PubMed

Joosten, R. P., Joosten, K., Murshudov, G. N. & Perrakis, A. (2012). PubMed PMC

Joosten, R. P., Long, F., Murshudov, G. N. & Perrakis, A. (2014). PubMed PMC

Joosten, R. P., Nicholls, R. A. & Agirre, J. (2022). PubMed PMC

Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., Back, T., Petersen, S., Reiman, D., Clancy, E., Zielinski, M., Steinegger, M., Pacholska, M., Berghammer, T., Bodenstein, S., Silver, D., Vinyals, O., Senior, A. W., Kavukcuoglu, K., Kohli, P. & Hassabis, D. (2021). PubMed PMC

Karplus, P. A. & Diederichs, K. (2012). PubMed PMC

Keegan, R. M., McNicholas, S. J., Thomas, J. M. H., Simpkin, A. J., Simkovic, F., Uski, V., Ballard, C. C., Winn, M. D., Wilson, K. S. & Rigden, D. J. (2018). PubMed PMC

Kovalevskiy, O., Nicholls, R. A., Long, F., Carlon, A. & Murshudov, G. N. (2018). PubMed PMC

Kovalevskiy, O., Nicholls, R. A. & Murshudov, G. N. (2016). PubMed PMC

Krissinel, E. & Henrick, K. (2007). PubMed

Krissinel, E., Lebedev, A. A., Uski, V., Ballard, C. B., Keegan, R. M., Kovalevskiy, O., Nicholls, R. A., Pannu, N. S., Skubák, P., Berrisford, J., Fando, M., Lohkamp, B., Wojdyr, M., Simpkin, A. J., Thomas, J. M. H., Oliver, C., Vonrhein, C., Chojnowski, G., Basle, A., Purkiss, A., Isupov, M. N., McNicholas, S., Lowe, E., Triviño, J., Cowtan, K., Agirre, J., Rigden, D. J., Uson, I., Lamzin, V., Tews, I., Bricogne, G., Leslie, A. G. W. & Brown, D. G. (2022).

Lamzin, V. S., Perrakis, A. & Wilson, K. S. (2012).

Langer, G., Cohen, S. X., Lamzin, V. S. & Perrakis, A. (2008). PubMed PMC

Lebedev, A. A. & Isupov, M. N. (2014). PubMed

Liebschner, D., Afonine, P. V., Baker, M. L., Bunkóczi, G., Chen, V. B., Croll, T. I., Hintze, B., Hung, L.-W., Jain, S., McCoy, A. J., Moriarty, N. W., Oeffner, R. D., Poon, B. K., Prisant, M. G., Read, R. J., Richardson, J. S., Richardson, D. C., Sammito, M. D., Sobolev, O. V., Stockwell, D. H., Terwilliger, T. C., Urzhumtsev, A. G., Videau, L. L., Williams, C. J. & Adams, P. D. (2019).

Long, F., Nicholls, R. A., Emsley, P., Gražulis, S., Merkys, A., Vaitkus, A. & Murshudov, G. N. (2017). PubMed PMC

Long, F., Vagin, A. A., Young, P. & Murshudov, G. N. (2008). PubMed PMC

Malý, M., Diederichs, K., Dohnálek, J. & Kolenko, P. (2020). PubMed PMC

McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007). PubMed PMC

McCoy, A. J., Oeffner, R. D., Wrobel, A. G., Ojala, J. R. M., Tryggvason, K., Lohkamp, B. & Read, R. J. (2017). PubMed PMC

McCoy, A. J., Sammito, M. D. & Read, R. J. (2022). PubMed PMC

McNicholas, S. & Agirre, J. (2017). PubMed PMC

McNicholas, S., Croll, T., Burnley, T., Palmer, C. M., Hoh, S. W., Jenkins, H. T., Dodson, E., Cowtan, K. & Agirre, J. (2018). PubMed PMC

McNicholas, S., Potterton, E., Wilson, K. S. & Noble, M. E. M. (2011). PubMed PMC

Medina, A., Jiménez, E., Caballero, I., Castellví, A., Triviño Valls, J., Alcorlo, M., Molina, R., Hermoso, J. A., Sammito, M. D., Borges, R. & Usón, I. (2022). PubMed PMC

Millán, C., Jiménez, E., Schuster, A., Diederichs, K. & Usón, I. (2020). PubMed PMC

Millán, C., Sammito, M. & Usón, I. (2015). PubMed PMC

Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011). PubMed PMC

Mylona, A., Carr, S., Aller, P., Moraes, I., Treisman, R., Evans, G. & Foadi, J. (2017). PubMed PMC

Nanao, M. H., Sheldrick, G. M. & Ravelli, R. B. G. (2005). PubMed

Newby, Z. E. R., O’Connell, J., Robles-Colmenares, Y., Khademi, S., Miercke, L. J. & Stroud, R. M. (2008). PubMed PMC

Nicholls, R. A. (2017). PubMed PMC

Nicholls, R. A., Fischer, M., McNicholas, S. & Murshudov, G. N. (2014). PubMed PMC

Nicholls, R. A., Joosten, R. P., Long, F., Wojdyr, M., Lebedev, A., Krissinel, E., Catapano, L., Fischer, M., Emsley, P. & Murshudov, G. N. (2021). PubMed PMC

Nicholls, R. A., Long, F. & Murshudov, G. N. (2012). PubMed PMC

Nicholls, R. A., Wojdyr, M., Joosten, R. P., Catapano, L., Long, F., Fischer, M., Emsley, P. & Murshudov, G. N. (2021). PubMed PMC

Noinaj, N., Easley, N. C., Oke, M., Mizuno, N., Gumbart, J., Boura, E., Steere, A. N., Zak, O., Aisen, P., Tajkhorshid, E., Evans, R. W., Gorringe, A. R., Mason, A. B., Steven, A. C. & Buchanan, S. K. (2012). PubMed PMC

Nolte, K., Gao, Y., Stäb, S., Kollmannsberger, P. & Thorn, A. (2022). PubMed PMC

Oeffner, R. D., Croll, T. I., Millán, C., Poon, B. K., Schlicksup, C. J., Read, R. J. & Terwilliger, T. C. (2022). PubMed PMC

Parkhurst, J. M. (2020). PhD thesis. University of Cambridge, United Kingdom. https://doi.org/10.17863/CAM.46755.

Parkhurst, J. M., Brewster, A. S., Fuentes-Montero, L., Waterman, D. G., Hattne, J., Ashton, A. W., Echols, N., Evans, G., Sauter, N. K. & Winter, G. (2014). PubMed PMC

Pearce, N. M., Krojer, T., Bradley, A. R., Collins, P., Nowak, R. P., Talon, R., Marsden, B. D., Kelm, S., Shi, J., Deane, C. M. & von Delft, F. (2017). PubMed PMC

Perrakis, A., Morris, R. & Lamzin, V. S. (1999). PubMed

Potterton, L., Agirre, J., Ballard, C., Cowtan, K., Dodson, E., Evans, P. R., Jenkins, H. T., Keegan, R., Krissinel, E., Stevenson, K., Lebedev, A., McNicholas, S. J., Nicholls, R. A., Noble, M., Pannu, N. S., Roth, C., Sheldrick, G., Skubak, P., Turkenburg, J., Uski, V., von Delft, F., Waterman, D., Wilson, K., Winn, M. & Wojdyr, M. (2018). PubMed PMC

Powell, H. R., Battye, T. G. G., Kontogiannis, L., Johnson, O. & Leslie, A. G. W. (2017). PubMed PMC

Rochira, W. & Agirre, J. (2021). PubMed PMC

Rodríguez, D. D., Grosse, C., Himmel, S., González, C., de Ilarduya, I. M., Becker, S., Sheldrick, G. M. & Usón, I. (2009). PubMed

Sammito, M. D., McCoy, A. J., Hatti, K., Oeffner, R. D., Stockwell, D. H., Croll, T. I. & Read, R. J. (2019). PubMed PMC

Sánchez Rodríguez, F., Chojnowski, G., Keegan, R. M. & Rigden, D. J. (2022). PubMed PMC

Sánchez Rodríguez, F., Mesdaghi, S., Simpkin, A. J., Burgos-Mármol, J. J., Murphy, D. L., Uski, V., Keegan, R. M. & Rigden, D. J. (2021). PubMed PMC

Sheldrick, G. M. (2008). PubMed

Shelley, K. L., Dixon, T. P. E., Brooks-Bartlett, J. C. & Garman, E. F. (2018). PubMed PMC

Shelley, K. L. & Garman, E. F. (2022). PubMed PMC

Simkovic, F., Thomas, J. M. H. & Rigden, D. J. (2017). PubMed PMC

Simpkin, A., Simkovic, F., Thomas, J., Savko, M., Ballard, C., Wojdyr, M., Shepard, W., Rigden, D. & Keegan, R. (2018). PubMed PMC

Simpkin, A. J., Elliott, L. G., Stevenson, K., Krissinel, E., Rigden, D. J. & Keegan, R. M. (2022).

Simpkin, A. J., Simkovic, F., Thomas, J. M. H., Savko, M., Lebedev, A., Uski, V., Ballard, C. C., Wojdyr, M., Shepard, W., Rigden, D. J. & Keegan, R. M. (2020). PubMed PMC

Simpkin, A. J., Thomas, J. M. H., Keegan, R. M. & Rigden, D. J. (2022). PubMed PMC

Skubák, P. & Pannu, N. S. (2013). PubMed PMC

Sobolev, O. V., Afonine, P. V., Moriarty, N. W., Hekkelman, M. L., Joosten, R. P., Perrakis, A. & Adams, P. D. (2020). PubMed PMC

Söding, J. (2005). PubMed

Steiner, R. A., Lebedev, A. A. & Murshudov, G. N. (2003). PubMed

Thorn, A., Parkhurst, J., Emsley, P., Nicholls, R. A., Vollmar, M., Evans, G. & Murshudov, G. N. (2017). PubMed PMC

Tickle, I. J. (2012). PubMed PMC

Touw, W. G., van Beusekom, B., Evers, J. M. G., Vriend, G. & Joosten, R. P. (2016). PubMed PMC

Trapani, S. & Navaza, J. (2008). PubMed PMC

Uervirojnangkoorn, M., Zeldin, O. B., Lyubimov, A. Y., Hattne, J., Brewster, A. S., Sauter, N. K., Brunger, A. T. & Weis, W. I. (2015). PubMed PMC

Usón, I. & Sheldrick, G. M. (2018). PubMed PMC

Vagin, A. A., Steiner, R. A., Lebedev, A. A., Potterton, L., McNicholas, S., Long, F. & Murshudov, G. N. (2004). PubMed

Vagin, A. & Lebedev, A. (2015).

Vagin, A. & Teplyakov, A. (2010). PubMed

Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., Žídek, A., Green, T., Tunyasuvunakool, K., Petersen, S., Jumper, J., Clancy, E., Green, R., Vora, A., Lutfi, M., Figurnov, M., Cowie, A., Hobbs, N., Kohli, P., Kleywegt, G., Birney, E., Hassabis, D. & Velankar, S. (2022). PubMed PMC

Westbrook, J. D., Shao, C., Feng, Z., Zhuravleva, M., Velankar, S. & Young, J. (2015). PubMed PMC

Williams, C. J., Headd, J. J., Moriarty, N. W., Prisant, M. G., Videau, L. L., Deis, L. N., Verma, V., Keedy, D. A., Hintze, B. J., Chen, V. B., Jain, S., Lewis, S. M., Arendall, W. B. III, Snoeyink, J., Adams, P. D., Lovell, S. C., Richardson, J. S. & Richardson, D. C. (2018). PubMed PMC

Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., McNicholas, S. J., Murshudov, G. N., Pannu, N. S., Potterton, E. A., Powell, H. R., Read, R. J., Vagin, A. & Wilson, K. S. (2011). PubMed PMC

Winter, G. (2010).

Winter, G., Lobley, C. M. C. & Prince, S. M. (2013). PubMed PMC

Winter, G., Waterman, D. G., Parkhurst, J. M., Brewster, A. S., Gildea, R. J., Gerstel, M., Fuentes-Montero, L., Vollmar, M., Michels-Clark, T., Young, I. D., Sauter, N. K. & Evans, G. (2018). PubMed PMC

Wojdyr, M. (2022).

Wojdyr, M., Keegan, R., Winter, G. & Ashton, A. (2013).

wwPDB Consortium (2019). PubMed PMC

Yamashita, K., Palmer, C. M., Burnley, T. & Murshudov, G. N. (2021). PubMed PMC

Yamashita, K., Wojdyr, M., Long, F., Nicholls, R. A. & Murshudov, G. N. (2023). PubMed PMC

Bispecific Thio-Linked Disaccharides as Inhibitors of Pseudomonas Aeruginosa Lectins LecA (PA-IL) and LecB (PA-IIL): Dual-Targeting Strategy

Novel archaeal ribosome dimerization factor facilitating unique 30S-30S dimerization

Substrate preference, RNA binding and active site versatility of Stenotrophomonas maltophilia nuclease SmNuc1, explained by a structural study