ConQuest User Guide and Tutorials 2016 CSDS Release Copyright © 2015 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, deCIFer, Mercury, (Mercury CSD and CSD-Materials [formerly known as the Solid Form or Materials module of Mercury], Mercury DASH), Mogul, IsoStar, DASH, 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, test versions of any existing or new program, code, tool, data files, sub-files, documentation or command procedures which may be available from time to time (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 or Products Licence and Support 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 Products Licence and Support 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 or Products Licence and Support 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 Certara and MDL is a registered trademark of BIOVIA) ii ConQuest User Guide and Tutorials Contents 1 The Cambridge Structural Database (CSD) ........................................................................1 1.1 Chemical Coverage of the CSD .............................................................................1 1.2 Literature Coverage of the CSD ............................................................................1 1.3 Database Entries...................................................................................................1 1.4 Refcodes (CSD Entry Identifiers) and Deposition Numbers..................................1 1.5 Information Content of the CSD...........................................................................2 1.5.1 Bibliographic Information in the CSD....................................................2 1.5.2 Chemical Information in the CSD ..........................................................2 1.5.3 Crystallographic Information in the CSD...............................................2 1.5.4 Text Information in the CSD..................................................................3 1.5.5 Filters: Secondary Search Criteria .........................................................3 1.6 A Typical CSD Entry...............................................................................................3 2 General Features of ConQuest ..........................................................................................6 2.1 The Basics of Using ConQuest ..............................................................................6 2.2 Building Queries: Overview ..................................................................................6 2.3 Storage of Queries During a ConQuest Session....................................................7 2.4 Use of Dialogue Boxes ..........................................................................................8 2.4.1 Typing into Input Boxes ........................................................................8 2.4.2 Case Sensitivity .....................................................................................9 2.4.3 Greyed-Out Buttons..............................................................................9 2.4.4 Mathematical Operators.......................................................................9 2.4.5 Closing and Resetting Dialogue Boxes ................................................10 2.5 Keyboard Shortcuts ............................................................................................10 2.6 Editing and Deleting Queries..............................................................................10 2.7 Saving and Reading Queries ...............................................................................10 2.8 Combining Queries .............................................................................................11 2.8.1 Reasons for Combining Queries..........................................................11 2.8.2 Simple Query Combinations ...............................................................11 2.8.3 Complex Query Combinations ............................................................12 2.9 Managing Hitlists ................................................................................................13 2.9.1 Hitlist Combinations............................................................................13 2.9.2 Saving and Reading Hitlist Combinations............................................15 2.9.3 Renaming, Annotating, Viewing and Deleting Hitlists ........................16 2.10 Starting Searches................................................................................................17 2.11 Naming Searches and Setting Filters ..................................................................18 2.12 Viewing Search Results.......................................................................................19 2.12.1 Monitoring Progress During a Search .................................................19 ConQuest User Guide and Tutorials iii 2.12.2 Selecting Individual Structures for Viewing ........................................19 2.12.3 Viewing Information for Individual Structures....................................20 2.12.4 Viewing the 2D Chemical Diagram......................................................21 2.12.5 Setting the Default Results Pane.........................................................22 2.12.6 Hyperlinking Between Entries.............................................................22 2.13 Using the 3D Visualiser.......................................................................................23 2.13.1 Visualiser Basics ..................................................................................23 2.13.2 Rotating, Translating and Scaling........................................................23 2.13.3 Changing Display Styles and Display of Hydrogen Atoms ...................23 2.13.4 Measuring Distances, Angles and Torsions.........................................24 2.13.5 Labelling Atoms...................................................................................24 2.13.6 Displaying Crystallographic Unit Cell Contents ...................................25 2.13.7 Highlighting Hit Fragments and Showing Results of Nonbonded Contact Searches.................................................................................25 2.13.8 Displaying 3D Parameters and Objects...............................................25 2.13.9 Saving Visualiser Images .....................................................................26 2.13.10 Saving Visualiser Settings....................................................................26 2.14 Displaying the Values of Defined Geometrical Parameters................................27 2.15 Switching between Searches..............................................................................27 2.16 Cancelling and Stopping Searches ......................................................................28 2.17 Suppressing Unwanted Entries...........................................................................28 2.18 Saving and Reading Searches .............................................................................28 2.19 Saving Individual Structures and Lists of Structures...........................................29 2.20 Transferring Data to Other Programs for Analysis .............................................30 2.20.1 Transferring Results Directly to Mercury’s statistical analysis package or Excel................................................................................................30