CAMERON [106], ORTEPIII [107], X-Seed [108] and Olex
2 [84]. CCDC
recognised the importance of crystal structure visualisation with the release of the
program Pluto [109] which was superseded in 2001 by the current visualisation and
analysis program Mercury [110, 111]. Mercury enables the visual exploration of
crystal structures and includes features such as the ability to generate packing
diagrams, build and explore networks of intermolecular contacts, display space
group symmetry elements and calculate and display voids and, since 2019, polyhedral display of metal-organic coordination compounds. Initially, any analysis of the
data had to be performed in external applications and then imported into a visualiser;
however, the launch of Vista in 1994 incorporated both these elements [112]. Vista
was later incorporated into Mercury as the data analysis module [113]. Further
developments to Mercury [114] included the ability to display ADPs, calculate
powder patterns, overlay two structures for the purpose of comparison and display
predicted crystal morphologies.
3.2.2 Database Searching
Initially the Molecular Structures and Dimensions book series provided a way for
chemists to look up structures based on bibliographic details and compound names,
much like an encyclopaedia. This allowed crystallographers to check which structures had previously been determined. In 1988 QUEST [115] was released and
provided integrated search facilities for text, numeric and 2D chemical information.
Notably it enabled chemical similarity and substructure searching for the first time
from a 2D sketcher. The graphical user interface was modernised in 2002 to the
program that is still in use today, ConQuest [110]. The power and versatility of
substructure searching has made it an invaluable research tool that has been a core
part of the CSD system ever since, and indeed the idea of not being able to search all
structures containing a drawn fragment would be challenging for many modern
research purposes. Today similarity searching is a common technique that is available in a number of programs, and there are several methods and coefficient scoring
measures that can be employed [116].
Information from the CSD can be used to inform the direction of new experiments. CellCheckCSD [117] is a command line tool for checking unit cells against
the known structures in the CSD during data collection, which allows a user to
determine if the compound is novel, accidental crystallisation of starting materials or
a reaction by-product. This has been integrated for automated for use through the
Rigaku software package CrysAlisPro and Bruker software suite APEX2, and its
utility in the experimental screening process is discussed in Sect. 1 [118].
The complexity of searches that may be performed has undergone a large shift in
the twenty-first century from the early simple ‘look-up’ searches to more advanced
searches which enable scientists to gain new insights from the data. One of the first
leaps was the addition of Motif searching [119] in 2004, in which a 2D substructure
search is followed by a 3D geometric search to find specific intermolecular interaction patterns. This capability was a significant tool that fuelled the growth of crystal
112
S. J. Coles et al.
2 [84]. CCDC
recognised the importance of crystal structure visualisation with the release of the
program Pluto [109] which was superseded in 2001 by the current visualisation and
analysis program Mercury [110, 111]. Mercury enables the visual exploration of
crystal structures and includes features such as the ability to generate packing
diagrams, build and explore networks of intermolecular contacts, display space
group symmetry elements and calculate and display voids and, since 2019, polyhedral display of metal-organic coordination compounds. Initially, any analysis of the
data had to be performed in external applications and then imported into a visualiser;
however, the launch of Vista in 1994 incorporated both these elements [112]. Vista
was later incorporated into Mercury as the data analysis module [113]. Further
developments to Mercury [114] included the ability to display ADPs, calculate
powder patterns, overlay two structures for the purpose of comparison and display
predicted crystal morphologies.
3.2.2 Database Searching
Initially the Molecular Structures and Dimensions book series provided a way for
chemists to look up structures based on bibliographic details and compound names,
much like an encyclopaedia. This allowed crystallographers to check which structures had previously been determined. In 1988 QUEST [115] was released and
provided integrated search facilities for text, numeric and 2D chemical information.
Notably it enabled chemical similarity and substructure searching for the first time
from a 2D sketcher. The graphical user interface was modernised in 2002 to the
program that is still in use today, ConQuest [110]. The power and versatility of
substructure searching has made it an invaluable research tool that has been a core
part of the CSD system ever since, and indeed the idea of not being able to search all
structures containing a drawn fragment would be challenging for many modern
research purposes. Today similarity searching is a common technique that is available in a number of programs, and there are several methods and coefficient scoring
measures that can be employed [116].
Information from the CSD can be used to inform the direction of new experiments. CellCheckCSD [117] is a command line tool for checking unit cells against
the known structures in the CSD during data collection, which allows a user to
determine if the compound is novel, accidental crystallisation of starting materials or
a reaction by-product. This has been integrated for automated for use through the
Rigaku software package CrysAlisPro and Bruker software suite APEX2, and its
utility in the experimental screening process is discussed in Sect. 1 [118].
The complexity of searches that may be performed has undergone a large shift in
the twenty-first century from the early simple ‘look-up’ searches to more advanced
searches which enable scientists to gain new insights from the data. One of the first
leaps was the addition of Motif searching [119] in 2004, in which a 2D substructure
search is followed by a 3D geometric search to find specific intermolecular interaction patterns. This capability was a significant tool that fuelled the growth of crystal
112
S. J. Coles et al.