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Mercury 2.4 User Guide and Tutorials 2011 CSDS Release

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Mercury 2.4 User Guide and Tutorials 2011 CSDS Release Mercury 2.4 User Guide and Tutorials 2011 CSDS Release Copyright © 2010 The Cambridge Crystallographic Data Centre Registered Charity No 800579 Conditions of Use The Cambridge Structural Database System (CSD System) comprising all or some of the following: ConQuest, Quest, PreQuest, Mercury, (Mercury CSD and Materials module of Mercury), VISTA, Mogul, IsoStar, SuperStar, web accessible CSD tools and services, WebCSD, CSD Java sketcher, CSD data file, CSD-UNITY, CSD-MDL, CSD-SDfile, CSD data updates, sub files derived from the foregoing data files, documentation and command procedures (each individually a Component) is a database and copyright work belonging to the Cambridge Crystallographic Data Centre (CCDC) and its licensors and all rights are protected. Use of the CSD System is permitted solely in accordance with a valid Licence of Access Agreement and all Components included are proprietary. When a Component is supplied independently of the CSD System its use is subject to the conditions of the separate licence. All persons accessing the CSD System or its Components should make themselves aware of the conditions contained in the Licence of Access Agreement or the relevant licence. In particular: • The CSD System and its Components are licensed subject to a time limit for use by a specified organisation at a specified location. • The CSD System and its Components are to be treated as confidential and may NOT be disclosed or re- distributed in any form, in whole or in part, to any third party. • Software or data derived from or developed using the CSD System may not be distributed without prior written approval of the CCDC. Such prior approval is also needed for joint projects between academic and for-profit organisations involving use of the CSD System. • The CSD System and its Components may be used for scientific research, including the design of novel compounds. Results may be published in the scientific literature, but each such publication must include an appropriate citation as indicated in the Schedule to the Licence of Access Agreement and on the CCDC website. • No representations, warranties, or liabilities are expressed or implied in the supply of the CSD System or its Components by CCDC, its servants or agents, except where such exclusion or limitation is prohibited, void or unenforceable under governing law. Licences may be obtained from: Cambridge Crystallographic Data Centre 12 Union Road Cambridge CB2 1EZ United Kingdom Web: http://www.ccdc.cam.ac.uk Telephone: +44-1223-336408 Email: [email protected] (UNITY is a product of Tripos, L.P. and MDL is a registered trademark of Elsevier MDL) Overview of Functionality (see page 6) Introduction to using Mercury (see page 9) Loading Structures (see page 20) Selecting and Displaying Structures (see page 25) Moving the Display and Setting the View Direction (see page 32) Customising the Display (see page 37) Centroids and Planes (see page 66) Measurement (see page 70) Crystal Structure Display Options (see page 71) Finding Hydrogen Bonds and other Nonbonded Contacts (see page 85) Building Networks of Nonbonded Contacts (see page 96) Editing a Structure (see page 106) Visualising CSD- and PDB-based Intermolecular Contact Distributions (see page 114) Geometry Validation (see page 119) Displaying Additional Information about the Structure (see page 125) Powder Diffraction Patterns (see page 141) Theoretical Calculations using MOPAC (see page 149) Saving Files and Copying to the Clipboard (see page 155) The Materials Module (see page 158) References (see page 188) Acknowledgements (see page 189) Appendix A: Glossary and Technical Details (see page 173) Appendix B: Keyboard Modifiers (see page 209) Appendix C: Tutorials (see page 211) Appendix D: What’s New (see page 289) Mercury User Guide 5 1 Overview of Functionality Mercury is a program for visualising crystal structures in three dimensions. Its features include: • The ability to read in crystal structures in various formats (see Loading Structures, page 20). • The ability to load hit lists from ConQuest searches, or to browse the entire Cambridge Structural Database (see Loading Structures, page 20). • The ability to show all the files that have been loaded in the current session, and navigate between them. • The ability to display multiple structures simultaneously (see Displaying Multiple Structures Simultaneously, page 27) and to perform least-squares overlay of pairs of structures (see Overlaying Crystal Structures, page 28) and pairs of chemically identical molecules (see Overlaying Molecules, page 29). • The ability to rotate and translate the 3D crystal-structure display, and to view down cell axes, reciprocal cell axes, and the normals to least-squares and Miller planes (see Moving the Display and Setting the View Direction, page 32). • A range of 3D visualisation options, including choice of display styles (wireframe, capped stick, ball and stick, spacefill and ellipsoid), colours, labelling schemes, and the ability to hide and then re-display atoms or molecules (see Customising the Display, page 37). • A display style manager that contains pre-defined styles (for presentations, publication etc.), and provides a mechanism for creating and modifying sets of Mercury display styles, which are automatically saved between sessions. • The ability to measure and display distances, angles and torsion angles involving atoms, centroids and planes (see Measurement, page 70). • The ability to create and display centroids, least-squares mean planes and Miller planes (see Centroids and Planes, page 66). • The ability to display unit cell axes, the contents of any number of unit cells in any direction, or a slice through a crystal in any direction (see Crystal Structure Display Options, page 71). • The ability to display of Bravais, Friedel, Donnay and Harker (BFDH) theoretical crystal morphologies (see Displaying Bravais, Friedel, Donnay and Harker (BFDH) Crystal Morphology, page 76). • Free space in crystal structures, or voids, can be calculated and displayed as coloured surfaces. Control over the calculation parameters and display options is also available (see Displaying Voids, page 81). • The ability to display space-group symmetry elements (see Displaying Space-Group Symmetry Elements, page 83). • Location and display of intermolecular and/or intramolecular hydrogen bonds, short nonbonded contacts, and user-specified types of contacts (e.g. between a specific pair of elements in a given distance range, which may be expressed in terms of absolute or van der Waals corrected distances) (see Finding Hydrogen Bonds and other Nonbonded Contacts, page 85). 6 Mercury User Guide • The ability to build and visualise a network of intermolecular contacts (see Building Networks of Nonbonded Contacts, page 96). • The ability to perform graph set analysis of hydrogen-bonding patterns (see Displaying Graph Sets, page 78). • The ability to show extra information about the structure on display, such as the chemical diagram (if available), atomic coordinates and the symmetry operations used to generate contacts (see Displaying Additional Information about the Structure, page 125). • The ability to manually edit structures including the addition of hydrogen atoms, the addition of bonds, the editing of bond types, the removal of atoms, bonds and molecules, the addition of atoms and the editing of atom types or labels (see Manually Editing a Structure, page 106). • The ability to automatically assign bond-types, standardise bond-types to Cambridge Structural Database conventions and to add missing hydrogen atoms (see Auto-Editing Options, page 108). • The ability to access CSD- and PDB based intermolecular contact distributions. Select atoms or contacts within the Mercury display to find IsoStar plots for the relevant contact groups. This can be used e.g. to validate the geometry of an H-bond or short range interaction within a crystal structure (see Visualising CSD- and PDB-based Intermolecular Contact Distributions, page 114). • The ability to run Mogul geometry checks from within Mercury, e.g. to validate the intramolecular geometries of newly determined crystal structures and identify unusual geometric features (see Geometry Validation, page 119). • The ability to calculate, display and save the powder diffraction pattern for the structure on view (see Powder Diffraction Patterns, page 141). • The ability to perform a limited number of molecule-based gas phase theoretical calculations using an interface to MOPAC (see MOPAC Calculations, page 149). • The ability to transform, invert or translate molecules or structures (see Transforming, Translating or Inverting Molecules, page 111) and the ability to change the space group setting (see Changing the Setting of a Space Group, page 113). • Materials module allowing: • Structural searches to be carried out to identify interaction motifs that occur between particular functional groups and determine their relative abundance (see Searching on Motifs, page 160). • Searches can also be performed by selecting atoms in a currently loaded crystal structure and searching for structures that contain a similar packing arrangement (see Searching on Crystal Packing Features, page 170). • Crystal packing similarity calculations can now be performed between structures containing the same compound (see Determining Crystal Packing Similarity, page 177). • The ability to save displays (see Saving Files and Copying to the Clipboard, page 155). • The ability to undo (reverse) previous action(s),
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