miniworkshop jan2003

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CCP4 Study Weekend 3rd January 2003 CCP4i - “Tricks and Tools” Peter Briggs CCP4 Daresbury

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CCP4i - “Tricks and Tools” Project Management Tools Project Directories Job Database & Project History Electronic Notebook Report External Tasks Data Harvesting File Viewers Loggraph MapSlicer AstexViewer Installing new tasks CCP4 Study Weekend 3rd January 2003 New in CCP4i 1.3.8 Preferences

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CCP4 Study Weekend 3rd January 2003 New in CCP4i 1.3.8 New interfaces: OASIS ACORN ANISOANL, TLSANL BEAST PROFESSS ROTAMER WHAT_CHECK (n.b. the program must currently be obtained from CMBI) New CCP4i-based application GET_PROT (aka SAPHIRE) download & edit protein sequence data Updated interfaces and tools: SCALA Import Scaled Data task Automatic reindexing facility in CAD task Integrated viewers (MapSlicer, AstexViewer) Task Interface Installer

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CCP4 Study Weekend 3rd January 2003 Why Project Management? Reminds you what you did six months ago Helps keep track of multiple projects and associated data Facilitates back-tracking (especially if things go wrong) Helps when depositing results & writing your paper Project Directories Set up aliases for project directories in “Project & Project Directories” Window All data files relating to one crystallographic project should be in a single project directory Job Database & Project History Stores parameters used to run each task Records input, output and logfiles for each job Allows you to review parameters used Allows you to rerun a job with the same/modified parameters Project Management Tools (1)

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CCP4 Study Weekend 3rd January 2003 Access additional tools through the “Edit Job Data” option: Electronic Notebook Record information about a particular job for future reference Edit Job Data Keep Job Database up-to-date Record changes e.g. of file locations Report External Tasks Record runs of non-CCP4(i) programs plus associated files Keep project history complete Project Management Tools (2)

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CCP4 Study Weekend 3rd January 2003 Why is it useful? Data is automatically collected in Harvest Files The files can be deposited directly, reducing the amount of manual handling at deposition What does it require? Harvesting Project & Dataset names must be defined in MTZ file Can be done at any entry point (e.g. “import” tasks) or via “Edit Project & Dataset Name” task How much work is it? Switch harvesting on (or off) in Preferences or in individual tasks That’s all Data Harvesting

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CCP4 Study Weekend 3rd January 2003 From within CCP4i: View Files from Job: always uses default file viewer View Any File: allows you to select from available viewers From Unix command line: Use ccp4i -v <filename> to view a file in the default viewer Useful for MTZ files (automatically runs mtzdump program to display header) HTML logfiles Can be viewed as plain text or in HTML browser Loggraph View tables and graphs in CCP4-formatted logfiles Can also use loggraph <filename> at the command line File Viewers (1)

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CCP4 Study Weekend 3rd January 2003 MapSlicer Interactive viewer for map sections Can view single sections or slabs on x, y or z axes Special mode for viewing Harker sections Can set this to be the default map viewer in “Preferences” File Viewers (2)

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CCP4 Study Weekend 3rd January 2003 AstexViewer Java-based protein-ligand viewer Displays structures in electron density Can be launched from “AstexViewer” task in Program List XtalView/Xfit launcher Also available for those who prefer to use XtalView - in “Model Building” module File Viewers (3)

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CCP4 Study Weekend 3rd January 2003 Installing New Tasks Install task interfaces supplied for non-CCP4i programs e.g. ARP/wARP 6.0 Accessed from “System Administration” menu New tasks installed in main CCP4i area (available to all) or in user’s “private” (i.e. $HOME/.CCP4/…, available only to that user) Allows easy review, update (and de-installation) of currently installed task interfaces

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CCP4 Study Weekend 3rd January 2003 CCP4i Preferences Set various useful things in the “Preferences”: Default viewers for maps & PDB files Default locations and formats for map files Default Data Harvesting mode

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CCP4 Study Weekend 3rd January 2003 Further Information … Project Management Tools: “CCP4i as a Project Management Tool” - CCP4 Newsletter 38 (April 2000) http://www.ccp4.ac.uk/newsletter38/09_projman.html MapSlicer: “MAPSLICER: an interactive viewer for contoured map sections” - CCP4 Newsletter 39 (March 2001) http://www.ccp4.ac.uk/newsletter39/09_mapslicer.html What’s New in CCP4i 1.3.8/Future Developments: “Developments with CCP4i” - CCP4 Newsletter 41 (October 2002) http://www.ccp4.ac.uk/newsletter41/02_ccp4i-oct02/ccp4i-oct2002.html CCP4i Webpage: http://www.ccp4.ac.uk/ccp4i_main.html

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CCP4 Study Weekend 3rd January 2003 Acknowledgements CCP4i was originally developed by Liz Potterton CCP4 Daresbury staff (Peter Briggs, Martyn Winn, Charles Ballard, Alun Ashton, Pryank Patel) AstexViewer developed by Mike Hartshorn of Astex Technologies Maria Turkenburg, Eleanor Dodson, Anne Baker & Everyone who has contributed ideas and comments!

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CCP4 Study Weekend 3rd January 2003 The End.