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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. - PowerPoint PPT Presentation
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• 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