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Status report

Status report. Data model for goniometry and collision maps CCPN-generated Java API (file-based backend) ‏ Used by: STAC: to persist a pure-rotation description of the goniostat and a set of collision maps for a range of detector distances

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Status report

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  1. Status report • Data model for goniometry and collision maps • CCPN-generated Java API (file-based backend)‏ • Used by: • STAC: to persist a pure-rotation description of the goniostat and a set of collision maps for a range of detector distances • BEST: to calculate a set of possible strategies exploiting Kappa geometry

  2. The future • Further testing and development • Extension of scope of model • All beamline instrumentation, not just goniostat • Output of strategy calculations, and data collection • Perform real data collections according to the calculated strategies • Collaboration between Global Phasing and Soleil

  3. People involved • Sándor Brockhauser • EMBL Grenoble • Johan Unge, Gleb Bourenkov • EMBL Hamburg • CCPN: Rasmus Fogh, Wayne Boucher, Ernest Laue • Biochemistry Department, Cambridge

  4. BioXDM coordinate systems • Described by: • The matrix required to convert from a canonical coordinate system • The incident beam direction • The component of the principal goniostat axis perpendicular to the beam • An orientation vector/matrix is: • A unit vector/orthogonal matrix with an associated coordinate system

  5. BioXDM goniometry model • Completely general multi-axis (not Kappa specific)‏ • Pure rotation • Each axis represented as direction (given by a unit vector) + setting • These directions may change from one data collection to another (e.g. By re-calibration)‏ • No account taken of physical motors or translations

  6. BioXDM collision map • The “axes” of the collision map are identified with “axes” of the goniostat • In the Kappa case, Omega and Kappa • A set of collision maps are stored, over several detector distances • A utility function provides an appropriate collision map for a specified detector distance • Each point on the map is an object in its own right

  7. BioXDM and data modelling • Why do data modelling? Reasons include: • Emphasis on science first, then implementation • In the BioXDM context, provides “glue” to connect diverse applications together • c.f. BEST and STAC

  8. BioXDM and CCPN • Currently use the CCPN approach • Python and Java API's are generated from the data model (with a small amount of hand-written code)‏ • API's perform a lot of data integrity checking (derived from data model) that would be tedious and impractical to code by hand.

  9. CCPN status • Java API now able to use an SQL backend via Hibernate (at least in prototype form)‏ • Python API only supports XML file backend • Rely on ObjectDomain for data modelling • this is an unsupported product

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