-- THURSDAY, 29 AUGUST 2019 --
KEYNOTE: CODATA, FAIR data and Open Science
The digital revolution has led to the transformation of a number of scientific disciplines. To take advantage of this and to accelerate the transformation, research communities and other stakeholders are calling for more appropriate and Open Science practices of scholarly communication and the implementation of the FAIR principles. CODATA is the Committee on Data of the International Science Council and has been involved in many of these developments. This talk will discuss these developments and introduce CODATA’s strategy to advance Open Science, help implement FAIR and to pursue the International Science Council’s new Science Action Plan. Particularly attention will be paid to recent work on data principles and practices, the need to develop data skills, the African Open Science Platform initiative and the ISC CODATA initiative to increase interoperability and use of data for cross-domain research addressing global challenges.
KEYNOTE: The science is in the data
The “Open Science” model is based on open access to published scientific results and on sharing scientific data according to the FAIR (Findable, Accessible, Interoperable and Re-usable) principles. The importance of archiving raw data underpinning crystallographic research and providing a permanent identifier is discussed. Different examples will be given where re-analysis of the data led to different conclusions, where raw data are needed because of questionable results and raw data are needed for methods development or for investigation with newly available tools.
VIDEO MESSAGE: Quality structural data in modern scientific culture
John R. Helliwell
The crystallographic community has always been particularly aware of the importance for sound data analysis and evaluation. Modern technology facilitates very high volumes and rates of data collection, and also provides ever improving tools for quality evaluation. Journals and databases have also been active in assuring high quality and, increasingly, in disseminating the experimental data that underpin structural models. In the modern research ecosystem, acronyms such as FAIR (Findable, Accessible, Interoperable, Re-usable) and FACT (Fair, Accurate, Confidential and Transparent) characterise community and society’s expectation of research data management. In this video presentation, John Helliwell, Chair of the IUCr Committee on Data and IUCr Representative to CODATA, explains how the IUCr guides the crystallographic community in the exercise of these principles.
KEYNOTE: The devil is in the detail
A historical account of the development of a standard exchange mechanism for crystallographic software. What began as an exercise in defining a common data exchange format has become a fully-featured Crystallographic Information Framework with wide-ranging uses in publishing, data validation and archiving.
-- FRIDAY, 30 AUGUST 2019 --
LAAAMP COLLOQUIUM: Planning diffraction experiments at large-scale facilities
This talk outlines the types of diffraction techniques typically available at synchrotron and neutron facilities. Guidance is provided on choosing the right technique for the experimental problem, developing an experimental plan, and optimal data collection strategies to maximise the benefit from the instrument time.
PLENARY: Data evaluation, integration and analysis I. Data evaluation
The data collection strategy is often already chosen based on the Bravais lattice. Several steps must be taken in data evaluation of the image data:
- Are the data from a single crystal? Are reflections from multiple lattices visible? If so, can we separate reflections from the different lattices? Do we have arbitrary lattice orientations, pseudo merohedral twinning or satellite reflections from incommensurate modulation?
- Do the images show diffuse scattering? This can be streaks, rings, triangles or cloudy diffuse scattering.
- Indexing of the crystal lattice(s) and refinement against the observed reflection spots on the images.
- Did we record the core metadata? Single spindle axis for rotation scan, three, four or six circle goniometer, beam position, detector distance etc.
Once the diffraction patterns are indexed the integrated intensities for each Bragg reflection should be determined
- Prediction of reflection positions. Instrument and crystal model: beam spectrum, beam divergence, crystal size, mosaic spread.
- Integration: fitting of the reflection profile in 2D or 3D, together with:
- Background model: background scattering, sample mount/capillary, dark current, read-out-noise
- Lorentz and polarization correction
Data evaluation, integration and analysis II. Data analysis
Evaluate the quality of the data. Given the Bravais lattice what is the data completeness, redundancy and maximum resolution?
- Scaling: bring all reflections and the same scale. Beam fluctuations, diffracting volume, absorption correction, radiation damage
- Merging reflection according to Laue symmetry: multiple scans
- Anomalous data: keep Bijvoet pairs separate
- Quality indicators: Rmerge, Rrim, Rpim, Ranom, CC1/2, I/σ
- Point group and space group needs to be determined for structure solution: extinctions
- Statistics for analyzing merohedral twinning and pseudo-translation
- Reciprocal space reconstruction: did we miss anything?
PLENARY: Space-group symmetry - understanding International Tables for Crystallography, Vol. A
Mois I. Aroyo
Volume A of International Tables for Crystallography (ITA) is the definitive resource and reference work on space-group symmetry. The aim of the lecture is to give a brief overview on the presentation of the space-group crystallographic data in ITA. The following main topics are included: (i) space-group symbolism (Schoenflies and Hermann-Mauguin); (ii) descriptions of symmetry operations (ITA and Seitz symbols of symmetry operations, symmetry-elements and general-position diagrams; (iii) asymmetric units and origins of space groups; (iv) general and special Wyckoff positions; (v) coordinate transformations in crystallography, conventional and nonconventional settings of space groups. Illustrative examples and didactic exercises complement the lecture material.
TUTORIAL: Crystallography online by the Bilbao Crystallographic Server
Mois I. Aroyo
The Bilbao Crystallographic Server (www.cryst.ehu.es) is a web site with crystallographic databases and programs. It can be used free of charge from any computer with a web browser via Internet. The aim of the tutorial is to give a practical guide with hands-on sessions to some of the computer tools available on the Bilbao Crystallographic Server for treating problems of theoretical crystallography, solid-state physics and crystal chemistry. The following topics will be discussed in more detail: (i) crystallographic groups (including sub periodic and magnetic) and their symmetry relationships; (ii) coordinate transformations in crystallography, and (iii) online tools for descriptions and comparison of crystal structures and their symmetry relationships.
-- SATURDAY, 31 AUGUST 2019 --
PLENARY: The CIF dictionaries: how they work
The general principles of CIF dictionaries are described, with details of how to extend the controlled vocabulary they provide for local purposes or for general community use.
- attributes associated with individual data items
- dictionary definition language (DDL) providing machine-readable access to these attributes
- DDL dialects and how they permit greater automation
- how to create new data items.
PLENARY: The central crystallographic ontology: core and mmCIF dictionaries
An overview is given of the core and mmCIF dictionaries and how they are arranged in categories related to different aspects of the crystallographic experiment. The core categories will be described in detail. mmCIF categories describing protein structure will be introduced in a general way for a plenary audience (more specific macromolecular structure considerations will be addressed in the presentation by J. Berrisford during the parallel sessions).
- experimental measurements
- analysis (structure solution and refinement)
- atomicity, chemistry and structure
- file metadata
-- SUNDAY, 1 SEPTEMBER 2019 --
PATH 1 (SMALL CELL PARAMETERS): Validation: Understanding CheckCIF for small molecules
A brief description of the historical background of, and motivation for, small-molecule structure validation is used to introduce the logical structure of CheckCIF and the categories of tests that it conducts. The corresponding categories of alerts are presented, and examples are given of selected alerts and appropriate actions in response to those alerts. Emphasis is placed throughout on the main issues addressed by CheckCIF:
- Completeness and self-consistency of the data provided in the CIF;
- Detection of errors or important deficiencies in the structure analysis;
- Estimation of the quality of the structure analysis.
The presentation concludes with a suggested strategy for practical and efficient use of structure validation in a small-molecule crystal structure analysis.
PATH 1 (SMALL CELL PARAMETERS): Publication: preparing small-molecule structure reports for IUCr journals
The lecture will give an overview of the main tools provided by the IUCr Journals for preparing a structural communication on small molecules in line with the quality and editorial requirements set by the Union. In particular, a description of the program publCIF will be given, which uses CIF files to directly format a paper in the style of Acta Crystallographica Sections C and E. Finally, some guidelines and best practice will be provided on how to efficiently organize a structural paper.
PATH 2 (MACROMOLECULES): Protein structure validation and quality assessment
Why protein structures need to be validated. The overdetermination problem. Validation and quality assessment. Parameters and tools that are usually monitored. Available validation servers
PATH 2 (MACROMOLECULES): Protein structure: instructions for use
Overview of biologically relevant information that could be derived from a three-dimensional structure of a protein. Possible examples: (a) from structure to function, (b) drug design and homology modelling, (c) definition of enzyme catalytic activity at atomic level, (d) principles governing protein-protein interactions
-- MONDAY, 2 SEPTEMBER 2019 --
PATH 1 (SMALL CELL PARAMETERS): Magnetic and incommensurate extension dictionaries
Mois I. Aroyo
Magnetic and incommensurate structures can be described using extension CIF dictionaries that help to codify their characteristics and form a basis for including such structures in their own specialised databases. The aim of the talk is to present a brief introduction to the extension CIF dictionaries of magnetic and incommensurate structures and their use in the structural databases of the Bilbao Crystallographic Server.
PATH 1 (SMALL CELL PARAMETERS): Small-molecule extension CIF dictionaries
An overview will be given of other dictionaries that extend the core crystallographic concepts, including treatment of twinning, refinement restraints and constraints, powder diffraction, electron density and modulated structures.
PATH 1 (SMALL CELL PARAMETERS): Other tools for submission of structure reports
Over the years IUCr journals have created a number of online tools to assist in the submission of structure report articles, though many can also be used to generate nicely formatted tables of data or molecular graphics suitable for use in theses or presentations.
PATH 2 (MACROMOLECULES): PDBx and related dictionaries
Following on from the brief introduction to the mmCIF dictionary in the plenary session, this lecture will explain the shortcomings of the legacy PDB file format, the great increase in the number of defined data items needed to meet all the requirements of the PDB, and the vigorous development of new extension dictionaries to accommodate methods like X-ray Free-Electron Laser (XFEL) and Serial Femtosecond Crystallography (SFX) and non -diffraction methods of protein structure determination.
- Limitation of PDB format and benefit of using mmcif over PDB
- Categories related to macromolecular crystallography
- Overview of mmcif dictionary content and organization
- Tools and resources to generate and convert mmcif
PATH 2 (MACROMOLECULES): Publishing biomacromolecule structures: requirements and opportunities
An overview of the standards required for publications. Policies of the journals that generally publish protein structures. Focus on the IUCr Journals.