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CSD Release & Installation Notes CSD Release and Installation Notes 2017 CSD Release Copyright © 2016 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 CSD Release and Installation Notes Contents 1 CSD Release Package .........................................................................................................1 2 Database Content and Information...................................................................................2 3 What’s New .......................................................................................................................3 4 Known Problems................................................................................................................4 5 Installation Overview.........................................................................................................5 5.2 System Requirements...........................................................................................5 5.2.1 Supported Platforms.............................................................................5 5.2.2 Changes to Supported Platforms ..........................................................5 5.2.3 Stereoscopic Viewing Graphical System Requirements........................6 5.2.4 Disk Space Requirements......................................................................6 6 Windows Installation.........................................................................................................7 6.1 General Installation Options.................................................................................7 6.2 Installation Procedure ..........................................................................................7 6.3 Uninstalling CSD System Software and Database files .........................................7 7 Linux Installation ...............................................................................................................8 7.1 Installation Procedure ..........................................................................................8 7.2 IsoStar 2.2.4 Server Installation............................................................................8 8 Mac OS X Installation.........................................................................................................9 8.1 General Installation Process .................................................................................9 8.2 Installation Procedure ..........................................................................................9 8.3 Troubleshooting ...................................................................................................9 9 WebCSD Access ...............................................................................................................10 9.1 CCDC Hosted WebCSD Server.............................................................................10 9.2 Locally Installed WebCSD Server ........................................................................10 10 Starting and Configuring CSD System Software...............................................................11 10.1 Windows.............................................................................................................11 10.2 Linux ...................................................................................................................11 10.3 Mac OS X.............................................................................................................11 10.4 Using Hermes to access GOLD, SuperStar and Relibase+ functionality..............12 10.4.1 Testing your Installation......................................................................12 10.5 Registration of CSD System Components...........................................................12 10.6 Configuration of CSD System Components ........................................................12 10.6.1 ConQuest ............................................................................................12 10.6.2 Mogul..................................................................................................13 10.6.3 Mercury...............................................................................................13 10.7 Setting up the CSD System Environment on Linux and Mac OS X ......................13 10.8 Unity desktop launchers for Ubuntu Linux.........................................................14 CSD Release and Installation Notes iii 11 CSD Python API................................................................................................................16 11.1 Use of the CSD Python API in Mercury ...............................................................16 11.2 Use of the CSD Python API via the command line..............................................16 11.2.1 Using the CSD Python API on Windows ..............................................16 11.2.2 Using the CSD Python API on Linux.....................................................16 11.2.3 Using the CSD Python API on Mac OS X ..............................................17 11.3 Use of the CSD Python API with your own Python installation ..........................17 12 CSD System Software Licensing.......................................................................................18 12.1 Licensing Overview.............................................................................................18 12.2 Registration Overview ........................................................................................18 12.3 Specifying an Existing Licence File ......................................................................19 12.4 Online Registration.............................................................................................20 12.5 Offline Registration.............................................................................................20 12.6 Batch registration tool........................................................................................22 12.6.1 Windows .............................................................................................22 12.6.2 Linux....................................................................................................22 12.6.3 Mac OS X .............................................................................................22 12.6.4 Advanced Use of the batch registration tool ......................................22 12.7 Registering the Different Mercury Components ................................................22 12.8 IP-Based Licensing ..............................................................................................23 12.9 Registration Problems ........................................................................................24
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