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Visualization Generation of reports, charts Data mining tools?
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Valle et al., NSMB 10 (2003) 899
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Flexible fitting of X-ray structures into cryo-EM maps: real space refinement Gao et al., Cell 113 (2003) 789-801.
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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
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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
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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
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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.
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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
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