http://journals.iucr.org/d/issues/2013/07/00/isscontsbdy.html Acta Crystallographica Section D: Biological Crystallography welcomes the submission of papers covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports on new protein structures are particularly encouraged, as are structure-function papers that could include crystallographic binding studies, or structural analysis of mutants or other modified forms of a known protein structure. The key criterion is that such papers should present new insights into biology, chemistry or structure. Papers on crystallographic methods should be oriented towards biological crystallography, and may include new approaches to any aspect of structure determination or analysis. Papers on the crystallization of biological molecules will be accepted providing that these focus on new methods or other features that are of general importance or applicability. en Copyright (c) 2013 International Union of Crystallography 2013-06-17 International Union of Crystallography International Union of Crystallography http://journals.iucr.org urn:issn:0907-4449 Acta Crystallographica Section D: Biological Crystallography welcomes the submission of papers covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports on new protein structures are particularly encouraged, as are structure-function papers that could include crystallographic binding studies, or structural analysis of mutants or other modified forms of a known protein structure. The key criterion is that such papers should present new insights into biology, chemistry or structure. Papers on crystallographic methods should be oriented towards biological crystallography, and may include new approaches to any aspect of structure determination or analysis. Papers on the crystallization of biological molecules will be accepted providing that these focus on new methods or other features that are of general importance or applicability. text/html Acta Crystallographica Section D: Biological Crystallography, Volume 69, Part 7, 2013 text monthly 1 2002-01-01T00:00+00:00 7 69 2013-06-17 Copyright (c) 2013 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography 1193 urn:issn:0907-4449 med@iucr.org June 2013 2013-06-17 http://journals.iucr.org/logos/rss10d.gif http://journals.iucr.org/d/issues/2013/07/00/isscontsbdy.html Still image http://scripts.iucr.org/cgi-bin/paper?ba5191 An overview of autoindexing diffraction images based on one-dimensional fast Fourier transforms is presented. The implementation of the algorithm in the Mosflm/iMosflm program suite is described with a discussion of practical issues that may arise and ways of assessing the success or failure of the procedure. Recent developments allow indexing of images that show multiple lattices, and several examples demonstrate the success of this approach in real cases. Copyright (c) 2013 International Union of Crystallography urn:issn:0907-4449 Powell, H.R. Johnson, O. Leslie, A.G.W. 2013-06-13 doi:10.1107/S0907444912048524 International Union of Crystallography The principles of one-dimensional FFT-based autoindexing of diffraction images are described together with practical issues that may arise. A procedure for indexing multiple lattices as implemented in iMosflm is presented. EN autoindexing multiple lattices Mosflm data processing An overview of autoindexing diffraction images based on one-dimensional fast Fourier transforms is presented. The implementation of the algorithm in the Mosflm/iMosflm program suite is described with a discussion of practical issues that may arise and ways of assessing the success or failure of the procedure. Recent developments allow indexing of images that show multiple lattices, and several examples demonstrate the success of this approach in real cases. text/html Autoindexing diffraction images with iMosflm text 7 69 2013-06-13 Copyright (c) 2013 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 0 0 http://scripts.iucr.org/cgi-bin/paper?ba5190 Following integration of the observed diffraction spots, the process of `data reduction' initially aims to determine the point-group symmetry of the data and the likely space group. This can be performed with the program POINTLESS. The scaling program then puts all the measurements on a common scale, averages measurements of symmetry-related reflections (using the symmetry determined previously) and produces many statistics that provide the first important measures of data quality. A new scaling program, AIMLESS, implements scaling models similar to those in SCALA but adds some additional analyses. From the analyses, a number of decisions can be made about the quality of the data and whether some measurements should be discarded. The effective `resolution' of a data set is a difficult and possibly contentious question (particularly with referees of papers) and this is discussed in the light of tests comparing the data-processing statistics with trials of refinement against observed and simulated data, and automated model-building and comparison of maps calculated with different resolution limits. These trials show that adding weak high-resolution data beyond the commonly used limits may make some improvement and does no harm. Copyright (c) 2013 International Union of Crystallography urn:issn:0907-4449 Evans, P.R. Murshudov, G.N. 2013-06-13 doi:10.1107/S0907444913000061 International Union of Crystallography The new scaling program AIMLESS is described and tests of refinements at different resolutions are compared with analyses from the scaling step. EN data reduction data scaling software data statistics Following integration of the observed diffraction spots, the process of `data reduction' initially aims to determine the point-group symmetry of the data and the likely space group. This can be performed with the program POINTLESS. The scaling program then puts all the measurements on a common scale, averages measurements of symmetry-related reflections (using the symmetry determined previously) and produces many statistics that provide the first important measures of data quality. A new scaling program, AIMLESS, implements scaling models similar to those in SCALA but adds some additional analyses. From the analyses, a number of decisions can be made about the quality of the data and whether some measurements should be discarded. The effective `resolution' of a data set is a difficult and possibly contentious question (particularly with referees of papers) and this is discussed in the light of tests comparing the data-processing statistics with trials of refinement against observed and simulated data, and automated model-building and comparison of maps calculated with different resolution limits. These trials show that adding weak high-resolution data beyond the commonly used limits may make some improvement and does no harm. text/html How good are my data and what is the resolution? text 7 69 2013-06-13 Copyright (c) 2013 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 0 0 http://scripts.iucr.org/cgi-bin/paper?ba5192 In macromolecular X-ray crystallography, typical data sets have substantial multiplicity. This can be used to calculate the consistency of repeated measurements and thereby assess data quality. Recently, the properties of a correlation coefficient, CC1/2, that can be used for this purpose were characterized and it was shown that CC1/2 has superior properties compared with `merging' R values. A derived quantity, CC*, links data and model quality. Using experimental data sets, the behaviour of CC1/2 and the more conventional indicators were compared in two situations of practical importance: merging data sets from different crystals and selectively rejecting weak observations or (merged) unique reflections from a data set. In these situations controlled `paired-refinement' tests show that even though discarding the weaker data leads to improvements in the merging R values, the refined models based on these data are of lower quality. These results show the folly of such data-filtering practices aimed at improving the merging R values. Interestingly, in all of these tests CC1/2 is the one data-quality indicator for which the behaviour accurately reflects which of the alternative data-handling strategies results in the best-quality refined model. Its properties in the presence of systematic error are documented and discussed. Copyright (c) 2013 International Union of Crystallography urn:issn:0907-4449 Diederichs, K. Karplus, P.A. 2013-06-15 doi:10.1107/S0907444913001121 International Union of Crystallography Making the most of hard-won data in protein crystallography: to keep or not to keep, that is the question. EN R value correlation coefficient data quality model quality outlier rejection In macromolecular X-ray crystallography, typical data sets have substantial multiplicity. This can be used to calculate the consistency of repeated measurements and thereby assess data quality. Recently, the properties of a correlation coefficient, CC1/2, that can be used for this purpose were characterized and it was shown that CC1/2 has superior properties compared with `merging' R values. A derived quantity, CC*, links data and model quality. Using experimental data sets, the behaviour of CC1/2 and the more conventional indicators were compared in two situations of practical importance: merging data sets from different crystals and selectively rejecting weak observations or (merged) unique reflections from a data set. In these situations controlled `paired-refinement' tests show that even though discarding the weaker data leads to improvements in the merging R values, the refined models based on these data are of lower quality. These results show the folly of such data-filtering practices aimed at improving the merging R values. Interestingly, in all of these tests CC1/2 is the one data-quality indicator for which the behaviour accurately reflects which of the alternative data-handling strategies results in the best-quality refined model. Its properties in the presence of systematic error are documented and discussed. text/html Better models by discarding data? text 7 69 2013-06-15 Copyright (c) 2013 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 0 0 http://scripts.iucr.org/cgi-bin/paper?ba5186 When protein crystals are submicrometre-sized, X-ray radiation damage precludes conventional diffraction data collection. For crystals that are of the order of 100 nm in size, at best only single-shot diffraction patterns can be collected and rotation data collection has not been possible, irrespective of the diffraction technique used. Here, it is shown that at a very low electron dose (at most 0.1 e− Å−2), a Medipix2 quantum area detector is sufficiently sensitive to allow the collection of a 30-frame rotation series of 200 keV electron-diffraction data from a single ∼100 nm thick protein crystal. A highly parallel 200 keV electron beam (λ = 0.025 Å) allowed observation of the curvature of the Ewald sphere at low resolution, indicating a combined mosaic spread/beam divergence of at most 0.4°. This result shows that volumes of crystal with low mosaicity can be pinpointed in electron diffraction. It is also shown that strategies and data-analysis software (MOSFLM and SCALA) from X-ray protein crystallography can be used in principle for analysing electron-diffraction data from three-dimensional nanocrystals of proteins. Copyright (c) 2013 International Union of Crystallography urn:issn:0907-4449 Nederlof, I. van Genderen, E. Li, Y.-W. Abrahams, J.P. 2013-06-15 doi:10.1107/S0907444913009700 International Union of Crystallography An ultrasensitive Medipix2 detector allowed the collection of rotation electron-diffraction data from single three-dimensional protein nanocrystals for the first time. The data could be analysed using the standard X-ray crystallography programs MOSFLM and SCALA. EN electron diffraction electron microscopy Medipix2 MOSFLM nanocrystals When protein crystals are submicrometre-sized, X-ray radiation damage precludes conventional diffraction data collection. For crystals that are of the order of 100 nm in size, at best only single-shot diffraction patterns can be collected and rotation data collection has not been possible, irrespective of the diffraction technique used. Here, it is shown that at a very low electron dose (at most 0.1 e− Å−2), a Medipix2 quantum area detector is sufficiently sensitive to allow the collection of a 30-frame rotation series of 200 keV electron-diffraction data from a single ∼100 nm thick protein crystal. A highly parallel 200 keV electron beam (λ = 0.025 Å) allowed observation of the curvature of the Ewald sphere at low resolution, indicating a combined mosaic spread/beam divergence of at most 0.4°. This result shows that volumes of crystal with low mosaicity can be pinpointed in electron diffraction. It is also shown that strategies and data-analysis software (MOSFLM and SCALA) from X-ray protein crystallography can be used in principle for analysing electron-diffraction data from three-dimensional nanocrystals of proteins. text/html A Medipix quantum area detector allows rotation electron diffraction data collection from submicrometre three-dimensional protein crystals text 7 69 2013-06-15 Copyright (c) 2013 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 0 0 http://scripts.iucr.org/cgi-bin/paper?ba5187 A processing pipeline for diffraction data acquired using the `serial crystallography' methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A detailed analysis of the nature and impact of indexing ambiguities is presented. Simulations of the Monte Carlo integration scheme, which accounts for the partially recorded nature of the diffraction intensities, are presented and show that the integration of partial reflections could be made to converge more quickly if the bandwidth of the X-rays were to be increased by a small amount or if a slight convergence angle were introduced into the incident beam. Copyright (c) 2013 International Union of Crystallography urn:issn:0907-4449 White, T.A. Barty, A. Stellato, F. Holton, J.M. Kirian, R.A. Zatsepin, N.A. Chapman, H.N. 2013-06-15 doi:10.1107/S0907444913013620 International Union of Crystallography A processing pipeline for diffraction data acquired using the `serial crystallography' methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. EN data processing free-electron lasers serial crystallography CrystFEL Cheetah A processing pipeline for diffraction data acquired using the `serial crystallography' methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A detailed analysis of the nature and impact of indexing ambiguities is presented. Simulations of the Monte Carlo integration scheme, which accounts for the partially recorded nature of the diffraction intensities, are presented and show that the integration of partial reflections could be made to converge more quickly if the bandwidth of the X-rays were to be increased by a small amount or if a slight convergence angle were introduced into the incident beam. text/html Crystallographic data processing for free-electron laser sources text 7 69 2013-06-15 Copyright (c) 2013 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 0 0 http://scripts.iucr.org/cgi-bin/paper?ba5185 Most macromolecular crystallography (MX) diffraction experiments at synchrotrons use a single-axis goniometer. This markedly contrasts with small-molecule crystallography, in which the majority of the diffraction data are collected using multi-axis goniometers. A novel miniaturized κ-goniometer head, the MK3, has been developed to allow macromolecular crystals to be aligned. It is available on the majority of the structural biology beamlines at the ESRF, as well as elsewhere. In addition, the Strategy for the Alignment of Crystals (STAC) software package has been developed to facilitate the use of the MK3 and other similar devices. Use of the MK3 and STAC is streamlined by their incorporation into online analysis tools such as EDNA. The current use of STAC and MK3 on the MX beamlines at the ESRF is discussed. It is shown that the alignment of macromolecular crystals can result in improved diffraction data quality compared with data obtained from randomly aligned crystals. Copyright (c) 2013 International Union of Crystallography urn:issn:0907-4449 Brockhauser, S. Ravelli, R.B.G. McCarthy, A.A. 2013-06-15 doi:10.1107/S0907444913003880 International Union of Crystallography Hardware and software solutions for MX data-collection strategies using the EMBL/ESRF miniaturized multi-axis goniometer head are presented. EN kappa goniometer crystal alignment data-collection strategies Most macromolecular crystallography (MX) diffraction experiments at synchrotrons use a single-axis goniometer. This markedly contrasts with small-molecule crystallography, in which the majority of the diffraction data are collected using multi-axis goniometers. A novel miniaturized κ-goniometer head, the MK3, has been developed to allow macromolecular crystals to be aligned. It is available on the majority of the structural biology beamlines at the ESRF, as well as elsewhere. In addition, the Strategy for the Alignment of Crystals (STAC) software package has been developed to facilitate the use of the MK3 and other similar devices. Use of the MK3 and STAC is streamlined by their incorporation into online analysis tools such as EDNA. The current use of STAC and MK3 on the MX beamlines at the ESRF is discussed. It is shown that the alignment of macromolecular crystals can result in improved diffraction data quality compared with data obtained from randomly aligned crystals. text/html The use of a mini-κ goniometer head in macromolecular crystallography diffraction experiments text 7 69 2013-06-15 Copyright (c) 2013 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 0 0 http://scripts.iucr.org/cgi-bin/paper?ba5194 The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required. Copyright (c) 2013 International Union of Crystallography urn:issn:0907-4449 Warren, A.J. Armour, W. Axford, D. Basham, M. Connolley, T. Hall, D.R. Horrell, S. McAuley, K.E. Mykhaylyk, V. Wagner, A. Evans, G. 2013-06-15 doi:10.1107/S0907444913011359 International Union of Crystallography A comparison of X-ray diffraction and radiographic techniques for the location and characterization of protein crystals is demonstrated on membrane protein crystals mounted within lipid cubic phase material. EN membrane proteins lipid cubic phase microradiography microtomography The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required. text/html Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging text 7 69 2013-06-15 Copyright (c) 2013 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 0 0 http://scripts.iucr.org/cgi-bin/paper?ba5196 X-ray crystallography is the method of choice to deduce atomic resolution structural information from macromolecules. In recent years, significant investments in structural genomics initiatives have been undertaken to automate all steps in X-ray crystallography from protein expression to structure solution. Robotic systems are widely used to prepare crystallization screens and change samples on synchrotron beamlines for macromolecular crystallography. The only remaining manual handling step is the transfer of the crystal from the mother liquor onto the crystal holder. Manual mounting is relatively straightforward for crystals with dimensions of >25 µm; however, this step is nontrivial for smaller crystals. The mounting of microcrystals is becoming increasingly important as advances in microfocus synchrotron beamlines now allow data collection from crystals with dimensions of only a few micrometres. To make optimal usage of these beamlines, new approaches have to be taken to facilitate and automate this last manual handling step. Optical tweezers, which are routinely used for the manipulation of micrometre-sized objects, have successfully been applied to sort and mount macromolecular crystals on newly designed crystal holders. Diffraction data from CPV type 1 polyhedrin microcrystals mounted with laser tweezers are presented. Copyright (c) 2013 International Union of Crystallography urn:issn:0907-4449 Wagner, A. Duman, R. Stevens, B. Ward, A. 2013-06-13 doi:10.1107/S090744491300958X International Union of Crystallography Optical trapping has successfully been applied to select and mount microcrystals for subsequent X-ray diffraction experiments. EN laser tweezers optical trapping microcrystals crystal manipulation sample holders X-ray crystallography is the method of choice to deduce atomic resolution structural information from macromolecules. In recent years, significant investments in structural genomics initiatives have been undertaken to automate all steps in X-ray crystallography from protein expression to structure solution. Robotic systems are widely used to prepare crystallization screens and change samples on synchrotron beamlines for macromolecular crystallography. The only remaining manual handling step is the transfer of the crystal from the mother liquor onto the crystal holder. Manual mounting is relatively straightforward for crystals with dimensions of >25 µm; however, this step is nontrivial for smaller crystals. The mounting of microcrystals is becoming increasingly important as advances in microfocus synchrotron beamlines now allow data collection from crystals with dimensions of only a few micrometres. To make optimal usage of these beamlines, new approaches have to be taken to facilitate and automate this last manual handling step. Optical tweezers, which are routinely used for the manipulation of micrometre-sized objects, have successfully been applied to sort and mount macromolecular crystals on newly designed crystal holders. Diffraction data from CPV type 1 polyhedrin microcrystals mounted with laser tweezers are presented. text/html Microcrystal manipulation with laser tweezers text 7 69 2013-06-13 Copyright (c) 2013 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 0 0 http://scripts.iucr.org/cgi-bin/paper?ba5189 Structure determinations for biological macromolecules that have no known structural antecedents typically involve the incorporation of heavier atoms than those found natively in biological molecules. Currently, selenomethionyl proteins analyzed using single- or multi-wavelength anomalous diffraction (SAD or MAD) data predominate for such de novo analyses. Naturally occurring metal ions such as zinc or iron often suffice in MAD or SAD experiments, and sulfur SAD has been an option since it was first demonstrated using crambin 30 years ago; however, SAD analyses of structures containing only light atoms (Zmax ≤ 20) have not been common. Here, robust procedures for enhancing the signal to noise in measurements of anomalous diffraction by combining data collected from several crystals at a lower than usual X-ray energy are described. This multi-crystal native SAD method was applied in five structure determinations, using between five and 13 crystals to determine substructures of between four and 52 anomalous scatterers (Z ≤ 20) and then the full structures ranging from 127 to 1200 ordered residues per asymmetric unit at resolutions from 2.3 to 2.8 Å. Tests were devised to assure that all of the crystals used were statistically equivalent. Elemental identities for Ca, Cl, S, P and Mg were proven by f′′ scattering-factor refinements. The procedures are robust, indicating that truly routine structure determination of typical native macromolecules is realised. Synchrotron beamlines that are optimized for low-energy X-ray diffraction measurements will facilitate such direct structural analysis. Copyright (c) 2013 International Union of Crystallography urn:issn:0907-4449 Liu, Q. Liu, Q. Hendrickson, W.A. 2013-06-13 doi:10.1107/S0907444913001479 International Union of Crystallography Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use in structure determination. Here, native SAD procedures are described for enhancing the signal to noise in anomalous diffraction by using multiple crystals are described. Five applications demonstrate that truly routine structure determination is possible without the need for heavy atoms. EN anomalous scattering multiple crystals phase determination sulfur SAD Structure determinations for biological macromolecules that have no known structural antecedents typically involve the incorporation of heavier atoms than those found natively in biological molecules. Currently, selenomethionyl proteins analyzed using single- or multi-wavelength anomalous diffraction (SAD or MAD) data predominate for such de novo analyses. Naturally occurring metal ions such as zinc or iron often suffice in MAD or SAD experiments, and sulfur SAD has been an option since it was first demonstrated using crambin 30 years ago; however, SAD analyses of structures containing only light atoms (Zmax ≤ 20) have not been common. Here, robust procedures for enhancing the signal to noise in measurements of anomalous diffraction by combining data collected from several crystals at a lower than usual X-ray energy are described. This multi-crystal native SAD method was applied in five structure determinations, using between five and 13 crystals to determine substructures of between four and 52 anomalous scatterers (Z ≤ 20) and then the full structures ranging from 127 to 1200 ordered residues per asymmetric unit at resolutions from 2.3 to 2.8 Å. Tests were devised to assure that all of the crystals used were statistically equivalent. Elemental identities for Ca, Cl, S, P and Mg were proven by f′′ scattering-factor refinements. The procedures are robust, indicating that truly routine structure determination of typical native macromolecules is realised. Synchrotron beamlines that are optimized for low-energy X-ray diffraction measurements will facilitate such direct structural analysis. text/html Robust structural analysis of native biological macromolecules from multi-crystal anomalous diffraction data text 7 69 2013-06-13 Copyright (c) 2013 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 0 0 http://scripts.iucr.org/cgi-bin/paper?ba5195 xia2 is an expert system for the automated reduction of macromolecular crystallography (MX) data employing well trusted existing software. The system can process a full MX data set consisting of one or more sequences of images at one or more wavelengths from images to structure-factor amplitudes with no user input. To achieve this many decisions are made, the rationale for which is described here. In addition, it is critical to support the testing of hypotheses and to allow feedback of results from later stages in the analysis to earlier points where decisions were made: the flexible framework employed by xia2 to support this feedback is summarized here. While the decision-making protocols described here were developed for xia2, they are equally applicable to interactive data reduction. Copyright (c) 2013 International Union of Crystallography urn:issn:0907-4449 Winter, G. Lobley, C.M.C. Prince, S.M. 2013-06-18 doi:10.1107/S0907444913015308 International Union of Crystallography The basis for decision making in the program xia2 is described, alongside the framework to support these protocols. Where appropriate, applications of these protocols to interactive data processing are highlighted. EN automation data reduction expert system xia2 xia2 is an expert system for the automated reduction of macromolecular crystallography (MX) data employing well trusted existing software. The system can process a full MX data set consisting of one or more sequences of images at one or more wavelengths from images to structure-factor amplitudes with no user input. To achieve this many decisions are made, the rationale for which is described here. In addition, it is critical to support the testing of hypotheses and to allow feedback of results from later stages in the analysis to earlier points where decisions were made: the flexible framework employed by xia2 to support this feedback is summarized here. While the decision-making protocols described here were developed for xia2, they are equally applicable to interactive data reduction. text/html Decision making in xia2 text 7 69 2013-06-18 Copyright (c) 2013 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 0 0 http://scripts.iucr.org/cgi-bin/paper?ba5193 Current pixel-array detectors produce diffraction images at extreme data rates (of up to 2 TB h−1) that make severe demands on computational resources. New multiprocessing frameworks are required to achieve rapid data analysis, as it is important to be able to inspect the data quickly in order to guide the experiment in real time. By utilizing readily available web-serving tools that interact with the Python scripting language, it was possible to implement a high-throughput Bragg-spot analyzer (cctbx.spotfinder) that is presently in use at numerous synchrotron-radiation beamlines. Similarly, Python interoperability enabled the production of a new data-reduction package (cctbx.xfel) for serial femtosecond crystallography experiments at the Linac Coherent Light Source (LCLS). Future data-reduction efforts will need to focus on specialized problems such as the treatment of diffraction spots on interleaved lattices arising from multi-crystal specimens. In these challenging cases, accurate modeling of close-lying Bragg spots could benefit from the high-performance computing capabilities of graphics-processing units. Copyright (c) 2013 International Union of Crystallography urn:issn:0907-4449 Sauter, N.K. Hattne, J. Grosse-Kunstleve, R.W. Echols, N. 2013-06-18 doi:10.1107/S0907444913000863 International Union of Crystallography The Computational Crystallography Toolbox (cctbx) is a flexible software platform that has been used to develop high-throughput crystal-screening tools for both synchrotron sources and X-ray free-electron lasers. Plans for data-processing and visualization applications are discussed, and the benefits and limitations of using graphics-processing units are evaluated. EN data processing reusable code multiprocessing cctbx Current pixel-array detectors produce diffraction images at extreme data rates (of up to 2 TB h−1) that make severe demands on computational resources. New multiprocessing frameworks are required to achieve rapid data analysis, as it is important to be able to inspect the data quickly in order to guide the experiment in real time. By utilizing readily available web-serving tools that interact with the Python scripting language, it was possible to implement a high-throughput Bragg-spot analyzer (cctbx.spotfinder) that is presently in use at numerous synchrotron-radiation beamlines. Similarly, Python interoperability enabled the production of a new data-reduction package (cctbx.xfel) for serial femtosecond crystallography experiments at the Linac Coherent Light Source (LCLS). Future data-reduction efforts will need to focus on specialized problems such as the treatment of diffraction spots on interleaved lattices arising from multi-crystal specimens. In these challenging cases, accurate modeling of close-lying Bragg spots could benefit from the high-performance computing capabilities of graphics-processing units. text/html New Python-based methods for data processing text 7 69 2013-06-18 Copyright (c) 2013 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 0 0 http://scripts.iucr.org/cgi-bin/paper?ba5197 While the majority of macromolecular X-ray data are currently collected using highly efficient beamlines at an ever-increasing number of synchrotrons, there is still a need for high-performance reliable systems for in-house experiments. In addition to crystal screening and optimization of data-collection parameters before a synchrotron trip, the home system allows the collection of data as soon as the crystals are produced to obtain the solution of novel structures, especially by the molecular-replacement method, and is invaluable in achieving the quick turnover that is often required for ligand-binding studies in the pharmaceutical industry. There has been a continuous evolution of X-ray sources, detectors and software developed for in-house use in recent years and a diverse range of tools for structural biology laboratories are available. An overview of the main directions of these developments and examples of specific solutions available to the macromolecular crystallography community are presented in this paper, showing that data collection `at home' is still an attractive proposition complementing the use of synchrotron beamlines. Copyright (c) 2013 International Union of Crystallography urn:issn:0907-4449 Skarzynski, T. 2013-06-18 doi:10.1107/S0907444913013619 International Union of Crystallography Recent developments in X-ray crystallographic hardware related to structural biology research are presented and discussed. EN macromolecular crystallography X-ray hardware data collection While the majority of macromolecular X-ray data are currently collected using highly efficient beamlines at an ever-increasing number of synchrotrons, there is still a need for high-performance reliable systems for in-house experiments. In addition to crystal screening and optimization of data-collection parameters before a synchrotron trip, the home system allows the collection of data as soon as the crystals are produced to obtain the solution of novel structures, especially by the molecular-replacement method, and is invaluable in achieving the quick turnover that is often required for ligand-binding studies in the pharmaceutical industry. There has been a continuous evolution of X-ray sources, detectors and software developed for in-house use in recent years and a diverse range of tools for structural biology laboratories are available. An overview of the main directions of these developments and examples of specific solutions available to the macromolecular crystallography community are presented in this paper, showing that data collection `at home' is still an attractive proposition complementing the use of synchrotron beamlines. text/html Collecting data in the home laboratory: evolution of X-ray sources, detectors and working practices text 7 69 2013-06-18 Copyright (c) 2013 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 0 0 http://scripts.iucr.org/cgi-bin/paper?ba5188 The ESRF has worked with, and provided services for, the pharmaceutical industry since the construction of its first protein crystallography beamline in the mid-1990s. In more recent times, industrial clients have benefited from a portfolio of beamlines which offer a wide range of functionality and beam characteristics, including tunability, microfocus and micro-aperture. Included in this portfolio is a small-angle X-ray scattering beamline dedicated to the study of biological molecules in solution. The high demands on throughput and efficiency made by the ESRF's industrial clients have been a major driving force in the evolution of the ESRF's macromolecular crystallography resources, which now include remote access, the automation of crystal screening and data collection, and a beamline database allowing sample tracking, experiment reporting and real-time at-a-distance monitoring of experiments. This paper describes the key features of the functionality put in place on the ESRF structural biology beamlines and outlines the major advantages of the interaction of the ESRF with the pharmaceutical industry. Copyright (c) 2013 International Union of Crystallography urn:issn:0907-4449 Malbet-Monaco, S. Leonard, G.A. Mitchell, E.P. Gordon, E.J. 2013-06-18 doi:10.1107/S0907444913001108 International Union of Crystallography The key features of the functionality facilitating proprietary use of the ESRF's structural biology beamlines are described, as are the major advantages, in terms of beamline evolution, of the interaction of the ESRF with the pharmaceutical industry. EN synchrotron MX beamlines proprietary access service data collection automation The ESRF has worked with, and provided services for, the pharmaceutical industry since the construction of its first protein crystallography beamline in the mid-1990s. In more recent times, industrial clients have benefited from a portfolio of beamlines which offer a wide range of functionality and beam characteristics, including tunability, microfocus and micro-aperture. Included in this portfolio is a small-angle X-ray scattering beamline dedicated to the study of biological molecules in solution. The high demands on throughput and efficiency made by the ESRF's industrial clients have been a major driving force in the evolution of the ESRF's macromolecular crystallography resources, which now include remote access, the automation of crystal screening and data collection, and a beamline database allowing sample tracking, experiment reporting and real-time at-a-distance monitoring of experiments. This paper describes the key features of the functionality put in place on the ESRF structural biology beamlines and outlines the major advantages of the interaction of the ESRF with the pharmaceutical industry. text/html How the ESRF helps industry and how they help the ESRF text 7 69 2013-06-18 Copyright (c) 2013 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 0 0 http://scripts.iucr.org/cgi-bin/paper?ba5199 Modern synchrotron beamlines offer instrumentation of unprecedented quality, which in turn encourages increasingly marginal experiments, and for these, as much as ever, the ultimate success of data collection depends on the experience, but especially the care, of the experimenter. A representative set of difficult cases has been encountered at the Structural Genomics Consortium, a worldwide structural genomics initiative of which the Oxford site currently deposits three novel human structures per month. Achieving this target relies heavily on frequent visits to the Diamond Light Source, and the variety of crystal systems still demand customized data collection, diligent checks and careful planning of each experiment. Here, an overview is presented of the techniques and procedures that have been refined over the years and that are considered synchrotron best practice. Copyright (c) 2013 International Union of Crystallography urn:issn:0907-4449 Krojer, T. Pike, A.C.W. von Delft, F. 2013-06-18 doi:10.1107/S0907444913013280 International Union of Crystallography This article gives an overview of techniques and procedures for efficient data collection at synchrotron sources. EN data collection data-collection strategy structural genomics Modern synchrotron beamlines offer instrumentation of unprecedented quality, which in turn encourages increasingly marginal experiments, and for these, as much as ever, the ultimate success of data collection depends on the experience, but especially the care, of the experimenter. A representative set of difficult cases has been encountered at the Structural Genomics Consortium, a worldwide structural genomics initiative of which the Oxford site currently deposits three novel human structures per month. Achieving this target relies heavily on frequent visits to the Diamond Light Source, and the variety of crystal systems still demand customized data collection, diligent checks and careful planning of each experiment. Here, an overview is presented of the techniques and procedures that have been refined over the years and that are considered synchrotron best practice. text/html Squeezing the most from every crystal: the fine details of data collection text 7 69 2013-06-18 Copyright (c) 2013 International Union of Crystallography Acta Crystallographica Section D: Biological Crystallography research papers 0 0