Robert M. Hanson

Jmol – a paradigm shift in crystallographic visualization

Recent advances in molecular and crystallographic visualization methods are allowing instructors unprecedented opportunities to enhance student learning using virtual models within a familiar web-browser context. In step with these advances, the latest versions of the Jmol molecular visualization applet offer capabilities that hold potential for revolutionizing the way students learn about symmetry, uncertainty and the overall enterprise of molecular structure determination.

Web servers and services for electrostatics calculations with APBS and PDB2PQR

APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal‐enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization of electrostatic potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/.

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

BackgroundThe Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards.ResultsThis contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry.ConclusionsWe show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community.

A toolkit for publishing enhanced figures

A description is provided of a software utility for creating interactive figures derived from crystal structures using the Java program Jmol.

Absolute stereochemistry of the triol moiety of gymnoprenols: a reinvestigation

Abstract The absolute configurations of the C-2 and C-3 positions of gymnoprenol A (1), gymnoprenol B (2), and gymnopilin (3) have been revised from 2S,3R to 2R,3S.

Visualization and processing of computed solid-state NMR parameters : MagresView and MagresPython

We introduce two open source tools to aid the processing and visualisation of ab-initio computed solid-state NMR parameters. The Magres file format for computed NMR parameters (as implemented in CASTEP v8.0 and QuantumEspresso v5.0.0) is implemented. MagresView is built upon the widely used Jmol crystal viewer, and provides an intuitive environment to display computed NMR parameters. It can provide simple pictorial representation of one- and two-dimensional NMR spectra as well as output a selected spin-system for exact simulations with dedicated spin-dynamics software. MagresPython provides a simple scripting environment to manipulate large numbers of computed NMR parameters to search for structural correlations.

Quaternion-based definition of protein secondary structure straightness and its relationship to Ramachandran angles.

We describe here definitions of “local helical axis” and “straightness” that are developed using a simple quaternion‐based analysis of protein structure without resort to least‐squares fitting. As part of this analysis, it is shown how quaternion differences can be visualized to depict accurately the local helical axis relating any two adjacent amino acid residues in standard, nonidealized proteins. Three different options for the definition of amino acid residue orientation in terms of quaternion frames are described. Two of these, the “Cα frame” and the “P frame,” are shown to be correlated strongly with a simple approximate measure derived solely from Ramachandran angles. The relationship between quaternion‐based straightness and recognized DSSP‐derived secondary structure motifs is discussed. Proteins 2011;

MAGNDATA: towards a database of magnetic structures. I. The commensurate case

A free web page under the name MAGNDATA, which provides detailed quantitative information on more than 400 published magnetic structures, has been made available at the Bilbao Crystallographic Server (http://www.cryst.ehu.es). It includes both commensurate and incommensurate structures. In the first article in this series, the information available on commensurate magnetic structures was presented [Gallego, Perez-Mato, Elcoro, Tasci, Hanson, Momma, Aroyo & Madariaga (2016). J. Appl. Cryst. 49, 1750–1776]. In this second article, the subset of the database devoted to incommensurate magnetic structures is discussed. These structures are described using magnetic superspace groups, i.e. a direct extension of the non-magnetic superspace groups, which is the standard approach in the description of aperiodic crystals. The use of magnetic superspace symmetry ensures a robust and unambiguous description of both atomic positions and magnetic moments within a common unique formalism. The point-group symmetry of each structure is derived from its magnetic superspace group, and any macroscopic tensor property of interest governed by this point-group symmetry can be retrieved through direct links to other programs of the Bilbao Crystallographic Server. The fact that incommensurate magnetic structures are often reported with ambiguous or incomplete information has made it impossible to include in this collection a good number of the published structures which were initially considered. However, as a proof of concept, the published data of about 30 structures have been re-interpreted and transformed, and together with ten structures where the superspace formalism was directly employed, they form this section of MAGNDATA. The relevant symmetry of most of the structures could be identified with an epikernel or isotropy subgroup of one irreducible representation of the space group of the parent phase, but in some cases several irreducible representations are active. Any entry of the collection can be visualized using the online tools available on the Bilbao server or can be retrieved as a magCIF file, a file format under development by the International Union of Crystallography. These CIF-like files are supported by visualization programs like Jmol and by analysis programs like JANA and ISODISTORT.

Programmatic conversion of crystal structures into 3D printable files using Jmol

BackgroundThree-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious. To overcome this limitation, we developed a programmatic method that allows for facile conversion of thousands of crystal structures directly into 3D printable files.ResultsA collection of over 30,000 crystal structures in crystallographic information file (CIF) format from the Crystallography Open Database (COD) were programmatically converted into 3D printable files (VRML format) using Jmol scripting. The resulting data file conversion of the 30,000 CIFs proceeded as expected, however some inconsistencies and unintended results were observed with co-crystallized structures, racemic mixtures, and structures with large counterions that led to 3D printable files not containing the desired chemical structure. Potential solutions to these challenges are considered and discussed. Further, a searchable Jmol 3D Print website was created that allows users to both discover the 3D file dataset created in this work and create custom 3D printable files for any structure in the COD.ConclusionsOver 30,000 crystal structures were programmatically converted into 3D printable files, allowing users to have quick access to a sizable collection of 3D printable crystal structures. Further, any crystal structure (>350,000) in the COD can now be conveniently converted into 3D printable file formats using the Jmol 3D Print website created in this work. The 3D Print website also allows users to convert their own CIFs into 3D printable files. 3D file data, scripts, and the Jmol 3D Print website are provided openly to the community in an effort to promote discovery and use of 3D printable crystal structures. The 3D file dataset and Jmol 3D Print website will find wide use with researchers and educators seeking to 3D print chemical structures, while the scripts will be useful for programmatically converting large database collections of crystal structures into 3D printable files.

DSSR-enhanced visualization of nucleic acid structures in Jmol

Abstract 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).