• Visualization

• Generation of reports, charts

• Data mining tools?

Valle et al., NSMB 10 (2003) 899

Flexible fitting of X-ray structures into cryo-EM maps: real space refinement

Gao et al., Cell 113 (2003) 789-801.

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

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

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

Example for an Angular Histogram

Norcum and Boisset (2002)

Distribution of particles found shown in a diagram of two Eulerian angles. The number of particlesfalling in a particular direction Is indicated by the size of the circles.

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