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Local squaring functions of non-spherical templates

Local squaring functions of non-spherical templates. Jeffrey ROACH Charles W. CARTER Jr. Local squaring functions. Measure likelihood that a given oriented fragment occupies position Models fragment translation and orientation For fixed orientation, quick to compute (FFT).

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Local squaring functions of non-spherical templates

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  1. Local squaring functions of non-spherical templates Jeffrey ROACH Charles W. CARTER Jr.

  2. Local squaring functions • Measure likelihood that a given oriented fragment occupies position • Models fragment translation and orientation • For fixed orientation, quick to compute (FFT)

  3. Method A- density modification • Build a probabilistic envelope from LSFs of different fragments • Modification/improvement of noisy electron-density • Works well for single atom fragments at high resolution

  4. Method B- iterated model building • Construct atomic model from well placed fragments • Use this atomic model to generate new phases (Fourier recycling) • Works well with single atom fragments at atomic resolution - 10o phase improvements/cycle

  5. Iterated real/reciprocal space (A+B) filtering is powerful for phasing • Shake ‘N Bake, Resolve, DM, ShelxD • Highly distributed • LSF: orientated fragment calculated independently • Interpreting LSFs: each point in unit cell can be considered individually • IBM Blade Server (hopefully)

  6. Multi-atom fragment libraries extend LSF to lower resolution Tetrahedral Ca Planar groups involving C=O

  7. Extended fragments to aid assembly Sequential templates Kolodney, Koehl, Guibas, & Levitt Tertiary templates Cammer & Tropsha

  8. Interpolating orientation • SU2 parameterization • Internal symmetry needs homogenous spaces • Local coordinates • Polynomial interpolation

  9. Examples • Random phase errors: experimentally derived phases for rusticyanin • Systematic phase errors: model biased phases

  10. New project • Shantanu SHARMA (IIT Kanpur) new structural comparison- geared to our purposes • Correlation between sequence and structure spaces • PCA of DALI scores unable to separate four major classes in SCOP • GenCompress distance useless on coding regions • Kolmogorov complexity ultimate unattainable selection of informative properties

  11. Zagoruiko: “Non-informative properties wash away compactness” … 40 39 38 36 35 0 36 34 28 3 2 0 4 3 0 7 6 5 4 0 7 6 5 0 9 8 0 33 32 10 5 4 3 … • Sequence of integers encodes Delaunay tetrahedralization • Rank statistics metaphor • Dynamic programming: identify regularities in integer sequence

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