Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: cctbx
https://packages.ecosyste.ms/registries/pypi.org/packages/cctbx
The Computational Crystallography Toolbox
1 version
Latest release: about 4 years ago
9 downloads last month
Papers Mentioning cctbx 58
10.1107/S1600577518016570
Automated data collection and real-time data analysis suite for serial synchrotron crystallographyCited by: 34
Author(s): Shibom Basu, Jakub Wojciech Kaminski, Ezequiel Panepucci, Chia‐Ying Huang, Rangana Warshamanage, Meitian Wang, Justyna Aleksandra Wojdyla
Software Mentions: 11
Published: almost 6 years ago
10.1002/pro.3299
Automating tasks in protein structure determination with the clipper python moduleCited by: 6
Author(s): Stuart McNicholas, Tristan I. Croll, Tom Burnley, Colin M. Palmer, Soon Wen Hoh, Huw T. Jenkins, E.J. Dodson, Kevin Cowtan, Jon Agirre
Software Mentions: 10
Published: about 7 years ago
10.1107/S2059798319011471
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in <i>Phenix</i>Cited by: 3,483
Author(s): Dorothée Liebschner, Pavel V. Afonine, Matthew L. Baker, G. Bunkóczi, V.B. Chen, Tristan I. Croll, Bradley J. Hintze, Li Wei Hung, Swati Jain, Airlie J. McCoy, Nigel W. Moriarty, Robert D. Oeffner, Billy K. Poon, Michael G. Prisant, R.J. Read, Jane S. Richardson, David C. Richardson, Massimo Sammito, Oleg Sobolev, Duncan H. Stockwell, Thomas C. Terwilliger, Alexandre Urzhumtsev, Lizbeth L. Videau, Christopher J. Williams, Paul D. Adams
Software Mentions: 8
Published: about 5 years ago
10.1107/S2059798317016035
<i>CCP</i>4<i>i</i>2: the new graphical user interface to the<i>CCP</i>4 program suiteCited by: 353
Author(s): Liz Potterton, Jon Agirre, Charles Ballard, Kevin Cowtan, E.J. Dodson, Phil Evans, Huw T. Jenkins, Ronan Keegan, Eugene Krissinel, Kyle Stevenson, А. А. Лебедев, Stuart McNicholas, Robert A. Nicholls, M.E.M. Noble, Navraj S. Pannu, Christian Roth, George M. Sheldrick, Pavol Skubák, J.P. Turkenburg, Ville Uski, Frank von Delft, David Waterman, K.S. Wilson, Martyn Winn, Marcin Wojdyr
Software Mentions: 8
Published: almost 7 years ago
10.1107/S2059798318004576
<i>KAMO</i>: towards automated data processing for microcrystalsCited by: 174
Author(s): Keitaro Yamashita, Kunio Hirata, Masaki Yamamoto
Software Mentions: 8
Published: over 6 years ago
10.1107/S2053273319011446
Bayesian machine learning improves single-wavelength anomalous diffraction phasingCited by: 10
Author(s): María-José García-Bonete, Gergely Katona
Software Mentions: 7
Published: about 5 years ago
10.1107/S2059798316002187
Diffraction-geometry refinement in the<i>DIALS</i>frameworkCited by: 146
Author(s): David Waterman, Graeme Winter, Richard J. Gildea, James M. Parkhurst, Aaron S. Brewster, Nicholas K. Sauter, Gwyndaf Evans
Software Mentions: 6
Published: over 8 years ago
10.1107/S0907444913000863
New Python-based methods for data processingCited by: 92
Author(s): Nicholas K. Sauter, Johan Hattne, Ralf W. Grosse‐Kunstleve, Nathaniel Echols
Software Mentions: 6
Published: over 11 years ago
10.1038/s41598-019-55777-5
Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical propertiesCited by: 7
Author(s): Viktor Ahlberg Gagnér, Ida Lundholm, María-José García-Bonete, Helena Rodilla, Ran Friedman, Vitali Zhaunerchyk, Gleb Bourenkov, Thomas R. Schneider, Jan Stake, Gergely Katona
Software Mentions: 6
Published: almost 5 years ago
10.1107/S0907444909052925
<i>PHENIX</i>: a comprehensive Python-based system for macromolecular structure solutionCited by: 19,578
Author(s): Paul D. Adams, Pavel V. Afonine, G. Bunkóczi, Vincent B. Chen, Ian Davis, Nathaniel Echols, Jeffrey J. Headd, Li Wei Hung, Gary J. Kapral, Ralf W. Grosse‐Kunstleve, Airlie J. McCoy, Nigel W. Moriarty, Robert D. Oeffner, Randy J. Read, David C. Richardson, Jane S. Richardson, Thomas C. Terwilliger, Peter H. Zwart
Software Mentions: 6
Published: almost 15 years ago
10.7554/eLife.05421
Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystalsCited by: 106
Author(s): Monarin Uervirojnangkoorn, Oliver B. Zeldin, A.Y. Lyubimov, Johan Hattne, Aaron S. Brewster, Nicholas K. Sauter, Axel T. Brunger, William I. Weis
Software Mentions: 5
Published: over 9 years ago
10.1186/s40679-016-0037-7
Data systems for the Linac coherent light sourceCited by: 27
Author(s): J. B. Thayer, D. S. Damiani, C. J. B. Ford, M. M. Dubrovin, I. Gaponenko, C.P. O'Grady, W. Kroeger, J. Pines, Thomas J Lane, A. Salnikov, Dieter K. Schneider, T. Tookey, M. Weaver, Chun Hong Yoon, A. Perazzo
Software Mentions: 5
Published: almost 8 years ago
10.1107/S1399004714017039
New methods for indexing multi-lattice diffraction dataCited by: 53
Author(s): Richard J. Gildea, David Waterman, James M. Parkhurst, Danny Axford, Geoff Sutton, David I. Stuart, Nicholas K. Sauter, Gwyndaf Evans, Graeme Winter
Software Mentions: 5
Published: about 10 years ago
10.1107/S0907444913022750
<i>Phaser.MRage</i>: automated molecular replacementCited by: 204
Author(s): G. Bunkóczi, Nathaniel Echols, Airlie J. McCoy, Robert D. Oeffner, Paul D. Adams, Randy J. Read
Software Mentions: 5
Published: about 11 years ago
10.1107/S0021889812017293
Graphical tools for macromolecular crystallography in<i>PHENIX</i>Cited by: 136
Author(s): Nathaniel Echols, Ralf W. Grosse‐Kunstleve, Pavel V. Afonine, G. Bunkóczi, Vincent B. Chen, Jeffrey J. Headd, Airlie J. McCoy, Nigel W. Moriarty, Randy J. Read, David C. Richardson, Jane S. Richardson, Thomas C. Terwilliger, Paul D. Adams
Software Mentions: 5
Published: over 12 years ago
10.1107/S1399004714028132
FEM: feature-enhanced mapCited by: 155
Author(s): Pavel V. Afonine, Nigel W. Moriarty, Marat Mustyakimov, Oleg Sobolev, Thomas C. Terwilliger, Dušan Turk, Alexandre Urzhumtsev, Paul D. Adams
Software Mentions: 5
Published: over 9 years ago
10.1107/S2059798318007726
Electron diffraction data processing with <i>DIALS</i>Cited by: 96
Author(s): Max T. B. Clabbers, Tim Gruene, James M. Parkhurst, Jan Pieter Abrahams, David Waterman
Software Mentions: 5
Published: over 6 years ago
10.1107/S2052252515006740
Serial snapshot crystallography for materials science with SwissFELCited by: 18
Author(s): Catherine Dejoie, Stef Smeets, Christian Baerlocher, Nobumichi Tamura, Philip Pattison, R. Abela, Lynne B. McCusker
Software Mentions: 4
Published: over 9 years ago
10.1107/S1600576717016600
CAPOW: a standalone program for the calculation of optimal weighting parameters for least-squares crystallographic refinementsCited by: 0
Author(s): Natalie T. Johnson, Holger Ott, Michael R. Probert
Software Mentions: 4
Published: almost 7 years ago
10.1107/S2059798318009324
New tools for the analysis and validation of cryo-EM maps and atomic modelsCited by: 536
Author(s): Pavel V. Afonine, Bruno P. Klaholz, Nigel W. Moriarty, Billy K. Poon, Oleg V. Sobolev, Thomas C. Terwilliger, Paul D. Adams, Alexandre Urzhumtsev
Software Mentions: 4
Published: about 6 years ago
10.1107/S2059798320015879
<i>CERES</i>: a cryo-EM re-refinement system for continuous improvement of deposited modelsCited by: 11
Author(s): Dorothée Liebschner, Pavel V. Afonine, Nigel W. Moriarty, Billy K. Poon, Vincent B. Chen, Paul D. Adams
Software Mentions: 4
Published: almost 4 years ago
10.1107/S2059798318017795
<i>ZOO</i>: an automatic data-collection system for high-throughput structure analysis in protein microcrystallographyCited by: 134
Author(s): Kunio Hirata, Keitaro Yamashita, Go Ueno, Yoshiaki Kawano, Kazuya Hasegawa, Takashi Kumasaka, Masaki Yamamoto
Software Mentions: 4
Published: almost 6 years ago
10.1107/S2059798320000443
Extending the scope of coiled-coil crystal structure solution by <i>AMPLE</i> through improved <i>ab initio</i> modellingCited by: 7
Author(s): Jens M. H. Thomas, Ronan Keegan, Daniel J. Rigden, Owen R. Davies
Software Mentions: 3
Published: over 4 years ago
10.1107/S2059798315013236
A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental errorCited by: 55
Author(s): Randy J. Read, Airlie J. McCoy
Software Mentions: 3
Published: over 8 years ago
10.1107/S2059798317017235
<i>DIALS</i>: implementation and evaluation of a new integration packageCited by: 750
Author(s): Graeme Winter, David Waterman, James M. Parkhurst, Aaron S. Brewster, Richard J. Gildea, Markus Gerstel, Luis Fuentes-Montero, M. Vollmar, Tara Michels-Clark, I.D. Young, Nicholas K. Sauter, Gwyndaf Evans
Software Mentions: 3
Published: almost 7 years ago
10.1107/S1600576716005720
Data processing pipeline for serial femtosecond crystallography at SACLACited by: 71
Author(s): Takanori Nakane, Yasumasa Joti, Kensuke Tono, Makina Yabashi, Eriko Nango, So Iwata, Ryuichiro Ishitani, Osamu Nureki
Software Mentions: 3
Published: over 8 years ago
10.1107/S2053273316018696
Asymmetry in serial femtosecond crystallography dataCited by: 11
Author(s): Amit Sharma, Linda C. Johansson, Elin Dunevall, Weixiao Yuan Wahlgren, Richard Neutze, Gergely Katona
Software Mentions: 3
Published: almost 8 years ago
10.1107/S0907444913015308
Decision making in<i>xia</i>2Cited by: 479
Author(s): Graeme Winter, C.M.C. Lobley, Stephen M. Prince
Software Mentions: 3
Published: over 11 years ago
10.1107/S1399004715000383
<i>Brickworx</i>builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density mapsCited by: 8
Author(s): Grzegorz Chojnowski, Tomasz Waleń, Paweł Piątkowski, Wojciech Potrzebowski, Janusz M. Bujnicki
Software Mentions: 3
Published: over 9 years ago
10.1107/S2052252519000927
Rigid-body motion is the main source of diffuse scattering in protein crystallographyCited by: 25
Author(s): T. de Klijn, Antoine M. M. Schreurs, Loes M. J. Kroon-Batenburg
Software Mentions: 3
Published: almost 6 years ago
10.1107/S2059798318002978
Determination of Patterson group symmetry from sparse multi-crystal data sets in the presence of an indexing ambiguityCited by: 19
Author(s): Richard J. Gildea, Graeme Winter
Software Mentions: 2
Published: over 6 years ago
10.1107/S2053273314022207
The anatomy of a comprehensive constrained, restrained refinement program for the modern computing environment –<i>Olex2</i>dissectedCited by: 1,018
Author(s): Luc J. Bourhis, Oleg V. Dolomanov, Richard J. Gildea, Judith A. K. Howard, Horst Puschmann
Software Mentions: 2
Published: almost 10 years ago
10.1107/S0907444913000462
Bulk-solvent and overall scaling revisited: faster calculations, improved resultsCited by: 70
Author(s): Pavel V. Afonine, Ralf W. Grosse‐Kunstleve, Paul D. Adams, Alexandre Urzhumtsev
Software Mentions: 2
Published: over 11 years ago
10.1107/S0907444913018167
Improving experimental phases for strong reflections prior to density modificationCited by: 7
Author(s): Monarin Uervirojnangkoorn, Rolf Hilgenfeld, Thomas C. Terwilliger, Randy J. Read
Software Mentions: 2
Published: about 11 years ago
10.1107/S2059798318002292
<i>Fragon</i>: rapid high-resolution structure determination from ideal protein fragmentsCited by: 23
Author(s): Huw T. Jenkins
Software Mentions: 2
Published: over 6 years ago
10.1107/S2059798319009392
Sequence assignment for low-resolution modelling of protein crystal structuresCited by: 22
Author(s): Grzegorz Chojnowski, Joana Pereira, Victor S. Lamzin
Software Mentions: 2
Published: over 5 years ago
10.1107/S2059798319008933
Prediction of models for ordered solvent in macromolecular structures by a classifier based upon resolution-independent projections of local feature dataCited by: 0
Author(s): Laurel Jones, Michael Tynes, Paul Smith
Software Mentions: 2
Published: over 5 years ago
10.1107/S2059798315022408
A new default restraint library for the protein backbone in<i>Phenix</i>: a conformation-dependent geometry goes mainstreamCited by: 36
Author(s): Nigel W. Moriarty, Dale E. Tronrud, Paul D. Adams, P.A. Karplus
Software Mentions: 2
Published: almost 9 years ago
10.1107/S0021889811041161
<i>iotbx.cif</i>: a comprehensive CIF toolboxCited by: 539
Author(s): Richard J. Gildea, Luc J. Bourhis, Oleg V. Dolomanov, Ralf W. Grosse‐Kunstleve, Horst Puschmann, Paul D. Adams, Judith A. K. Howard
Software Mentions: 2
Published: about 13 years ago
10.1107/S1600576714011996
<i>dxtbx</i>: the diffraction experiment toolboxCited by: 26
Author(s): James M. Parkhurst, Aaron S. Brewster, Luis Fuentes-Montero, David Waterman, Johan Hattne, Alun Ashton, Nathaniel Echols, Gwyndaf Evans, Nicholas K. Sauter, Graeme Winter
Software Mentions: 2
Published: over 10 years ago
10.1107/S1600576715010432
Programming new geometry restraints: parallelity of atomic groupsCited by: 13
Author(s): Oleg Sobolev, Pavel V. Afonine, Paul D. Adams, Alexandre Urzhumtsev
Software Mentions: 2
Published: over 9 years ago
10.1107/S1600576716013595
Robust background modelling in <i>DIALS</i>Cited by: 43
Author(s): James M. Parkhurst, Graeme Winter, David Waterman, Luis Fuentes-Montero, Richard J. Gildea, Garib N. Murshudov, Gwyndaf Evans
Software Mentions: 2
Published: about 8 years ago
10.1107/S205225251402702X
Serial femtosecond crystallography: the first five yearsCited by: 259
Author(s): Ilme Schlichting
Software Mentions: 2
Published: almost 10 years ago
10.1016/j.jsb.2014.12.002
Seeing tobacco mosaic virus through direct electron detectorsCited by: 82
Author(s): Simon A. Fromm, Tanmay A. M. Bharat, Arjen J. Jakobi, Wim J. H. Hagen, Carsten Sachse
Software Mentions: 2
Published: almost 10 years ago
10.1107/S1600576716006981
On the release of<i>cppxfel</i>for processing X-ray free-electron laser imagesCited by: 29
Author(s): H. Ginn, Gwyndaf Evans, Nicholas K. Sauter, David I. Stuart
Software Mentions: 1
Published: over 8 years ago
10.1107/S1600577514028203
XFEL diffraction: developing processing methods to optimize data qualityCited by: 82
Author(s): Nicholas K. Sauter
Software Mentions: 1
Published: almost 10 years ago
10.1107/S2059798316013048
From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendumCited by: 3
Author(s): Alexandre Urzhumtsev, Pavel V. Afonine, A.H. Van Benschoten, James S. Fraser, Paul D. Adams
Software Mentions: 1
Published: about 8 years ago
10.1107/S160057671900342X
Full-profile search–match by the Rietveld methodCited by: 37
Author(s): Luca Lutterotti, Henry Pillière, Christophe Fontugne, Philippe Boullay, Daniel Chateigner
Software Mentions: 1
Published: over 5 years ago
10.1107/S2059798320000455
The use of local structural similarity of distant homologues for crystallographic model building from a molecular-replacement solutionCited by: 14
Author(s): Grzegorz Chojnowski, Koushik Choudhury, Philipp Heuser, E. V. Sobolev, Joana Pereira, Umut Oezugurel, Victor S. Lamzin
Software Mentions: 1
Published: over 4 years ago
10.1107/S2059798321007324
Versatile microporous polymer-based supports for serial macromolecular crystallographyCited by: 6
Author(s): Isabelle Martiel, John Beale, A. Karpik, Chia‐Ying Huang, Laura Vera, Natacha Olieric, Maximilian Wranik, Ching‐Ju Tsai, Jonas Mühle, Oskar Aurelius, Juliane John, Martin Högbom, Meitian Wang, M. Marsh, Celestino Padeste
Software Mentions: 1
Published: over 3 years ago
10.1107/S2059798320016332
The accuracy of protein models automatically built into cryo-EM maps with <i>ARP</i>/<i>wARP</i>Cited by: 14
Author(s): Grzegorz Chojnowski, E. V. Sobolev, Philipp Heuser, Victor S. Lamzin
Software Mentions: 1
Published: almost 4 years ago
10.1107/S2059798321002369
Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulationCited by: 0
Author(s): Ariana Peck, Qing Yao, Aaron S. Brewster, Petrus H. Zwart, John M. Heumann, Nicholas K. Sauter, Grant J. Jensen
Software Mentions: 1
Published: over 3 years ago
10.1107/S1399004714026145
Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patternsCited by: 17
Author(s): Aaron S. Brewster, M.R. Sawaya, José A. Rodríguez, Johan Hattne, Nathaniel Echols, Heather T. McFarlane, Duilio Cascio, Paul D. Adams, David Eisenberg, Nicholas K. Sauter
Software Mentions: 1
Published: almost 10 years ago
10.1107/S2052252520005916
Paired refinement under the control of<i>PAIREF</i>Cited by: 17
Author(s): Martin Malý, Kay Diederichs, Jan Dohnálek, Petr Kolenko
Software Mentions: 1
Published: over 4 years ago
10.1107/S1399004714024134
Improved crystal orientation and physical properties from single-shot XFEL stillsCited by: 39
Author(s): Nicholas K. Sauter, Johan Hattne, Aaron S. Brewster, Nathaniel Echols, Petrus H. Zwart, Paul D. Adams
Software Mentions: 1
Published: almost 10 years ago
10.1107/S1600576715012169
<i>Xtal-xplore-R</i>: a graphical tool for exploring the residual function involved in crystal structure determinationCited by: 0
Author(s): Jan Marten Simons, Georg Roth
Software Mentions: 1
Published: over 9 years ago
10.1042/BSR20170227
X-ray data processingCited by: 20
Author(s): Harold R. Powell
Software Mentions: 1
Published: about 7 years ago
10.1107/S1600576716006683
<i>IOTA</i>: integration optimization, triage and analysis tool for the processing of XFEL diffraction imagesCited by: 18
Author(s): A.Y. Lyubimov, Monarin Uervirojnangkoorn, Oliver B. Zeldin, Aaron S. Brewster, Thomas D. Murray, Nicholas K. Sauter, James M. Berger, William I. Weis, Axel T. Brunger
Software Mentions: 1
Published: over 8 years ago