1. Visualization Generation of reports, charts Data mining tools?

2. Valle et al., NSMB 10 (2003) 899

3. Flexible fitting of X-ray structures into cryo-EM maps: real space refinement Gao et al., Cell 113 (2003) 789-801.

4. L1 Stalk: “gatekeeper”, highly mobile, shuttles tRNA from P/E site to E site, and out of the ribosome. L7/L12 Stalk: highly mobile “molecular whip”, switches its conformation from an extended, unstructured form to a stabile rod. Stalk base: the base of the L7/L12 stalk, contains GTPase-associated center (GAC), changes orientation upon factor binding. Latch: a flexible connection between head and shoulder of the small subunit, forming the entrance channel for mRNA. Platform: in prokaryotes, contains Shine-Dalgarno sequence, recognized by mRNA during initiation. Sarcin-ricin loop: highly conserved binding site of factors on the 50S subunit J. Frank, Genome Biology 4 (2004) 237 helix 44 SRL

5. Visualization tools Quick look Examination with different modalities of viewing (rotating display, surface rendered, as contour, volume- rendered; as slices) Joint representation of density map with X-ray coos (semi-transparent, with fitted structure) X-ray coos low-pass filtered for comparison with density map Present segmented volume as defined by 3D masks Modes of interactive viewing: (1) steer viewing direction, angles reported; (2) dial angles to define viewing direction Same options available for related 3D maps, e.g., variance map. Joint viewing in corresponding directions

6. Reports Generation of spreadsheets and charts to view important parameters of the deposition Examples: refinement history, defocus distribution Classification dendrograms 3D density histograms Angular distribution

7. Example for an Angular Histogram Norcum and Boisset (2002) Distribution of particles found shown in a diagram of two Eulerian angles. The number of particles falling in a particular direction Is indicated by the size of the circles.

8. Data mining? 3D motif search/automated docking –with motifs supplied by the user of the data base –with motifs selected from the pdb –with motifs that are themselves density maps Wait