An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-molecule refinement and SHELXS and SHELXD are often employed for structure solution despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromolecules against high-resolution or twinned data; SHELXPRO acts as an interface for macromolecular applications. SHELXC, SHELXD and SHELXE are proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.

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A short history of SHELX

The program Mercury, developed by the Cambridge Crystallographic Data Centre, is designed primarily as a crystal structure visualization tool. A new module of functionality has been produced, called the Materials Module, which allows highly customizable searching of structural databases for intermolecular interaction motifs and packing patterns. This new module also includes the ability to perform packing similarity calculations between structures containing the same compound. In addition to the Materials Module, a range of further enhancements to Mercury has been added in this latest release, including void visualization and links to ConQuest, Mogul and IsoStar.

Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures

The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal–organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.

https://journals.iucr.org/b/issues/2016/02/00/bm5086/bm5086.pdf

The Cambridge Structural Database

The program Mercury, developed at the Cambridge Crystallographic Data Centre, was originally designed primarily as a crystal structure visualization tool. Over the years the fields and scientific communities of chemical crystallography and crystal engineering have developed to require more advanced structural analysis software. Mercury has evolved alongside these scientific communities and is now a powerful analysis, design and prediction platform which goes a lot further than simple structure visualization.

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Mercury 4.0: from visualization to analysis, design and prediction

Perovskite solar cells (PSCs) with efficiencies greater than 20% have been realized only with expensive organic hole-transporting materials. We demonstrate PSCs that achieve stabilized efficiencies exceeding 20% with copper(I) thiocyanate (CuSCN) as the hole extraction layer. A fast solvent removal method enabled the creation of compact, highly conformal CuSCN layers that facilitate rapid carrier extraction and collection. The PSCs showed high thermal stability under long-term heating, although their operational stability was poor. This instability originated from potential-induced degradation of the CuSCN/Au contact. The addition of a conductive reduced graphene oxide spacer layer between CuSCN and gold allowed PSCs to retain >95% of their initial efficiency after aging at a maximum power point for 1000 hours under full solar intensity at 60°C. Under both continuous full-sun illumination and thermal stress, CuSCN-based devices surpassed the stability of spiro-OMeTAD–based PSCs.

https://science.sciencemag.org/content/sci/early/2017/09/27/science.aam5655.full.pdf

Perovskite solar cells with CuSCN hole extraction layers yield stabilized efficiencies greater than 20

Since its original release, the popular crystal structure visualization program Mercury has undergone continuous further development. Comparisons between crystal structures are facilitated by the ability to display multiple structures simultaneously and to overlay them. Improvements have been made to many aspects of the visual display, including the addition of depth cueing, and highly customizable lighting and background effects. Textual and numeric data associated with structures can be shown in tables or spreadsheets, the latter opening up new ways of interacting with the visual display. Atomic displacement ellipsoids, calculated powder diffraction patterns and predicted morphologies can now be shown. Some limited molecular-editing capabilities have been added. The object-oriented nature of the C++ libraries underlying Mercury makes it easy to re-use the code in other applications, and this has facilitated three-dimensional visualization in several other programs produced by the Cambridge Crystallographic Data Centre.

Mercury: visualization and analysis of crystal structures

The enCIFer program permits the location, reporting and correction of syntax and format violations in single- or multi-block crystallographic information files (CIFs). The program also permits the editing of existing individual or looped data items and the addition of new data in these categories, and provides data-entry wizards for the addition of two types of standard information for small-molecule structural studies, namely publication data and chemical and physical property information. Facilities for the graphical visualization and manipulation of structure(s) in a CIF are also provided.

/pdf/cif-applications-xv-encifer-a-program-for-viewing-editing-4jznj78t2n.pdf

CIF applications. XV. enCIFer: a program for viewing, editing and visualizing CIFs

A transport stream of a compressed video signal is monitored. Information elements extracted from the transport stream prompt the generation of messages which are assigned a predetermined priority dependent upon their pre-determined criticality to integrity of the video signal. The generated messages are queued for analysis by analyzer modules only if their priority exceeds a current value of a variable threshold priority level for the queue. The variable threshold priority level is varied dependent on the current length of the queue. When the threshold level is raised, messages already in the queue having a lower priority than the new threshold priority are discarded from the queue without analysis. Thus a varying proportion of the least important messages are progressively discarded so that the apparatus continuously stabilizes at a maximum proportion of messages that the monitor can handle without overload, while always analyzing messages corresponding to the most critical parameters of the transport stream.

Analyzing a transport stream

Communicating science is hard. This is particularly true for a lot of structural science concepts which are inherently three dimensional in nature such as molecular geometry, symmetry, intermolecular interactions and the packing of crystal structures. One of the most effective ways to get around this difficulty is to use physical 3D models for communication, whether it is in an outreach setting, through classroom education or even presenting research results at a conference. Recent studies have shown how to generate instruction files to 3D print experimentally accurate models. Here we present for the first time how scientists can do this from any standard structural model file (incl. MOL2, XYZ, SDF, PDB, CIF, RES) easily using the well-known, freely available structure visualisation program, Mercury.

Matthew Towler

Papers

Mercury: visualization and analysis of crystal structures

Mercury 4.0: from visualization to analysis, design and prediction

CIF applications. XV. enCIFer: a program for viewing, editing and visualizing CIFs

Analyzing a transport stream

The next dimension of structural science communication: simple 3D printing directly from a crystal structure