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Visualization Generation of reports, charts Data mining tools?

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.

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Visualization Generation of reports, charts Data mining tools?

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  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 formRNA. 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 SRL helix 44 J. Frank, Genome Biology 4 (2004) 237

  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

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