Recent updates to the Jmol program have added significant capabilities for crystallographic visualization and education, specifically in the area of space groups and model building. Using either the Jmol Java application or its web-based JavaScript equivalent, one can can quickly build a model given a space group and setting, generate atoms at any of the Wyckoff positions, color atoms by position or site, display all the symmetry elements within a unit cell, and generate representations of the transformations that relate any two atoms or molecules. Built-in commands allow structure retrieval from external databases including the Crystallography Open Database, American Mineralogist Crystal Structure Database, and the AFLOW Encyclopedia of Crystallographic Prototypes. Atoms can be manipulated interactively, and the positions of all symmetry-related atoms are updated with constraints for atoms on special positions. In this talk we will demonstrate some of these new features and suggest ways that both the standalone application and simple web pages can be used to engage students and help them develop a deeper understanding of crystallography.

In this first of a two-part series, we introduce the concept of a FAIRSpec-ready spectroscopic data collection – that is, a collection of instrument data, chemical structure representations, and related digital items that is ready to be automatically or semi-automatically extracted for metadata that will allow the production of an IUPAC FAIRSpec Finding Aid. Associating this finding aid with the collection produces an IUPAC FAIRSpec Data Collection. The challenge we set for researchers is relatively simple: to maintain their data in a form that allows critical metadata to be extracted in a discipline-specific way, increasing the probability that the data will be findable and reusable both during the research process and after publication. We focus on a few specific suggestions that researchers can use to maximize the “fairness” of their spectroscopic data collection. Most importantly, following these guidelines ensures that instrument datasets are unambiguously associated with chemical structure. The guidelines promote the inclusion of the instrument dataset itself in the collection and describe ways of organizing the collection such that automated metadata creation is possible. In these guidelines we emphasize the importance of systematically organizing data throughout the entire research process, not just at the time of publication.

A concise machine-readable description of group settings and group-subgroup relations is proposed. The simple proposal allows for unambiguous generalized machine-coded space group settings and inter-group transformation relationships. The notation has been implemented in the Jmol Java and JavaScript application and library and is scriptable via the Jmol crystallographic MODELKIT command. The notation allows for Hermann-Mauguin or Hall notation but does not require them, provided the International Tables default space group settings are known.

Online courses and innovative teaching methods have triggered a trend in education, where the integration of multimedia, online resources and interactive tools is reshaping the view of both virtual and traditional classrooms. The use of interactive tools extends beyond the boundaries of the physical classroom, offering students the flexibility to access materials at their own speed and convenience and enhancing their learning experience. In the field of crystallography, there are a wide variety of free online resources such as web pages, interactive applets, databases and programs that can be implemented in fundamental crystallography courses for different academic levels and curricula. This paper discusses a variety of resources that can be helpful for crystallographic symmetry handling and visualization, discussing four specific resources in detail: the Bilbao Crystallographic Server, the Cambridge Structural Database, VESTA and Jmol. The utility of these resources is explained and shown by several illustrative examples.

The International Tables Symmetry Database (https://symmdb.iucr.org/), which is part of International Tables for Crystallography , is a collection of individual databases of crystallographic space-group and point-group information with associated programs. The programs let the user access and in some cases interactively visualize the data, and some also allow new data to be calculated `on the fly'. Together these databases and programs expand upon and complement the symmetry information provided in International Tables for Crystallography Volume A, Space-Group Symmetry , and Volume A1, Symmetry Relations between Space Groups . The Symmetry Database allows users to learn about and explore the space and point groups, and facilitates the study of group–subgroup relations between space groups, with applications in determining crystal-structure relationships, in studying phase transitions and in domain-structure analysis. The use of the International Tables Symmetry Database in all these areas is demonstrated using several examples.

The JCAMP-DX format is the most widely used vendor-independent data standard in spectroscopy. Based on the ASCII character set, the first standard was published for infrared spectroscopy in 1988 and over the years additional standards have been published covering most of the major spectroscopic techniques. This paper provides an overview of the JCAMP-DX standards, including a brief historical review. This is followed by a basic description of the format, example applications and a discussion of its continuing evolution.

A set of guiding principles for the development of a standard for FAIR management of spectroscopic data are outlined and discussed. The principles form the basis for future recommendations of IUPAC Project 2019-031-1-024 specifying a detailed data model and metadata schema for describing the contents of an "IUPAC FAIRData Collection" and the organization of digital objects within that collection. Foremost among the recommendations will be a specification for an "IUPAC FAIRData Finding Aid" that describes the collection in such a way as to optimize the findability, accessibility, interoperability, and reusability of its contents. Results of an analysis of data provided by an American Chemical Society Publications pilot study are discussed in relation to potential workflows that might be used in implementing the "IUPAC FAIRSpec" standard based on these principles.

Electrophoresis is a fundamental tool for biochemistry and molecular biology research. Our team has updated a popular 1D electrophoresis simulation to give instructors a choice ‐ they can use the built in protein mixtures or they can add their own protein mixtures and use the simulation to focus on particular learning goals and objectives in their classroom and laboratory courses. The simulation retains many of its original features: variable voltage and % acrylamide, built in molecular weight standards, animation of the pipetting process, and a built‐in plot for estimating molecular weights. Features in the updated simulation include (a) an expansion from two to ten wells, (b) drag and drop options for loading proteins on the gel, (c) a choice of ten built‐in protein sets and learning objectives designed for the BASIL curriculum (https://basilbiochem.github.io/basil/index.html), and (d) the option to introduce custom designed protein mixtures with associated learning objectives. The simulation, formerly a Java applet, was redeveloped using java2script/SwingJS and now runs both as an independent Java application and as a browser‐based JavaScript app.

Physlets, educational applets developed at Davidson College, are a widely used teaching resource designed to simulate a variety of physical phenomena. Originally, each Physlet was a Java simulation that was embedded in an HTML page as an applet and then customized using JavaScript to simulate a specific physics concept. The use of Java to simulate the physics and HTML + JavaScript to add narrative and to customize the web page allowed teachers to create thousands of Physlet-based illustrations, explorations, and problems. Unfortunately, changes in technology standards have required a drastic change in how these learning resources can be delivered.

The Tony Davies Column offers a challenge to us all with another contribution on FAIR data, which should be Findable, Available, Interoperable and Readable. It is clearly the way we should all be going, everybody from manufacturers and software developers, through researchers to publishers needs to work together.

We have successfully developed the technology used to produce JSmol with Jmol [1, 2] to produce JalviewJS with Jalview [3] for the integration and visualisation of biological sequence and three-dimensional structures and other data within an evolutionary alignment framework. java2script/SwingJS [4] has been used to produce well over 600 JavaScript apps from Java code bases involving over 5000 Java classes (including Java applets and full Java applications -- see, for example, Physlet Physics [5] and SwingJS Examples [6]). This is not a "total rewrite". This is a minor tweaking of a Java program to be "JavaScript compatible" with automated co-production of Java class files and their JavaScript equivalents simultaneously. java2script/SwingJS is breakthrough technology that allows open-source developers to produce multiple flavors of their programs (Java desktop power application, fully contextualized JavaScript web page-based embedded app, and self-contained progressive web app) from the same Java code base. Little or no actual programming is done in JavaScript. The java2script transpiler rides along with the Eclipse Java compiler to produce the JavaScript "class" files, which then "run" on a web page using the SwingJS equivalent of the Java Virtual Machine. We will discuss how this technology allows the Jalview Desktop (3000+ Java classes) to be used within a rich web-based environment, and how easy it is for any developer to do this themselves. [1] https://sourceforge.net/projects/jmol/files/Jmol [2] https://github.com/BobHanson/Jmol-SwingJS [3] http://www.jalview.org/ [4] https://github.com/BobHanson/java2script [5] https://www.compadre.org/physlets [6] https://chemapps.stolaf.edu/swingjs/site/swingjs/examples

The traditional paradigm for materials discovery has been recently expanded to incorporate substantial data driven research. With the intent to accelerate the development and the deployment of new technologies, the AFLOW Fleet for computational materials design automates high-throughput first principles calculations, and provides tools for data verification and dissemination for a broad community of users. AFLOW incorporates different computational modules to robustly determine thermodynamic stability, electronic band structures, vibrational dispersions, thermo-mechanical properties and more. The AFLOW data repository is publicly accessible online at aflow.org, with more than 1.7 million materials entries and a panoply of queryable computed properties. Tools to programmatically search and process the data, as well as to perform online machine learning predictions, are also available.

The most recent version of the Cahn-Ingold-Prelog rules for the determination of stereodescriptors as described in Nomenclature of Organic Chemistry: IUPAC Recommendations and Preferred Names 2013 (the “Blue Book”) were analyzed by an international team of cheminformatics software developers. Algorithms for machine implementation were designed, tested, and cross-validated. Deficiencies in Sequence Rules 1b and 2 were found, and proposed language for their modification is presented. A concise definition of an additional rule (“Rule 6,” below) is proposed, which succinctly covers several cases only tangentially mentioned in the 2013 recommendations. Each rule is discussed from the perspective of machine implementation. The four resultant implementations are supported by validation suites in 2D and 3D SDF format as well as SMILES. The validation suites include all significant examples in Chapter 9 of the Blue Book, as well as several additional structures that highlight more complex aspects of the rules not addressed or not clearly analyzed in that work. These additional structures support a case for the need for modifications of the Sequence Rules.

The many evolving variations of the Crystallographic Information Format pose substantial challenges for developers of tools such as Jmol that read and write a wide variety of file formats.Jmol, for instance, has been developed to handle parsing of standard "CIF1" format as well as macromolecular (mmCIF), magnetic (magCIF), and modulated structure (msCIF) formats, including their combinations, such data files for incommensurately modulated magnetic structures.In addition, Jmol must read similar information from non-CIF formats -PDB, and MMTF for macromolecular data; Jana2006 for incommensurately modulated structures.For maintenance purposes as well as the preservation of developer sanity, a layered approach was taken for the design of these readers in Jmol.Thus, the basic CIF1 reader is "subclassed" to become a CIF2 or mmCIF reader and fitted with relevant parsers for CIF1, CIF2, and specialized [3+n] modulation-related data.The result is a complex but manageable set of modules that work seamlessly to provide a unified crystallographic package.This presentation will focus on challenges in working with CIF1 and CIF2 formats, the development of a JSON version of these formats for testing purposes, and limitations in Jmol in relation to their implementations.

Many aspects of crystallography are difficult for students to conceptualize.Examples include symmetry operations, primitive vs. conventional unit cells, reciprocal lattices, electron density, incommensurate modulation, and local atom environments.Jmol, both as a stand-alone Java application and especially as its web-based HTML5/JavaScript "JSmol" equivalent, is uniquely positioned to provide dynamic, interactive, accessible opportunities to students and professionals alike so that they can explore and visualize these difficult concepts.This presentation will focus on recent developments in Jmol that allow students and interested developer-educators to address long-standing issues in crystallography education, providing examples of several simple web sites that have been developed or are in the process of development for such purposes.

An easily available resource of common crystal structures is essential for researchers, teachers, and students. For many years this was provided by the U.S. Naval Research Laboratory's Crystal Lattice Structures web page, which contained nearly 300 crystal structures, including a majority of those which were given Strukturbericht designations. This article presents the updated version of the database, now including 288 standardized structures in 92 space groups. Similar to what was available on the web page before, we present a complete description of each structure, including the formulas for the primitive vectors, all of the basis vectors, and the AFLOW commands to generate the standardized cells. We also present a brief discussion of crystal systems, space groups, primitive and conventional lattices, Wyckoff positions, Pearson symbols and Strukturbericht designations. The web version of this database is located at http://aflow.org/CrystalDatabase.

Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org).