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 …