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EM Database Data integration

The EMDB provides a robust platform for integrating and coordinating protein crystallography software through the CCP4 interface. It offers validated tools based on bond geometry and free R-factor, alongside a complete repository that features user-friendly visualization and sophisticated searching capabilities. Both novices and experts benefit from a well-designed interface with extensive validation information, including links to PDB and experimental data. Desirable features include advanced map manipulation tools and integration with cell structure data for enhanced structural analysis.

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EM Database Data integration

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  1. EM Database Data integration

  2. Role model – protein crystallography CCP4 – common interface to coordinate and integrate most of the software in the field; workshops, training; well established validation tools based on bond geometry, free R factor PDB – Complete public repository with user-friendly visualization and integration tools, sophisticated searching, validation information, used by experts and non-specialists

  3. Basic featuresfor the EMDB • A nice front page – for both novice and expert users • Searching on entry number, author, keyword,.. • A friendly data page with a picture of the map • Bug-free map header • Links to sequence and function databases • Experimental information • Validation information • Links to and from the PDB

  4. Desirable featuresfor the EMDB • A Rasmol for maps • Tools for moving and aligning maps • A button to shift the EM map from the center of the box to the origin of the coordinate system, needed for symmetry operations and for matching up with pdb files • Searching densities by cross correlation • Integrate with cell structure data • Validation with Rosenthal/Henderson tilt data • Fold searching for maps at <7 Å • Full integration into the PDB

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