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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). - PowerPoint PPT Presentation
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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)
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
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
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)
Multi-atom fragment libraries extend LSF to lower resolution
Planar groups involving C=O
Tetrahedral C
Extended fragments to aid assembly
Sequential templatesKolodney, Koehl, Guibas, & Levitt
Tertiary templatesCammer & Tropsha
Interpolating orientation
SU2 parameterization Internal symmetry needs
homogenous spaces Local coordinates Polynomial interpolation
Examples
Random phase errors: experimentally derived phases for rusticyanin
Systematic phase errors: model biased phases
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
Zagoruiko: “Non-informative properties wash away compactness”
Sequence of integers encodes Delaunay tetrahedralization Rank statistics metaphor Dynamic programming: identify regularities in integer
sequence
… 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 …