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Presentation transcript:

Free download with instructions A Brief Instruction to VEC Hua Jiang Free download with instructions and examples at http://cryst.iphy.ac.cn

The big picture d dI dI Phases inside inner sphere Phases between Amplitudes inside two spheres Phases between two spheres Phase extension D d dI dI structure

far from the Scherzer defocus Deconvolution of a Single EM far from the Scherzer defocus Original image Image of the final model Image after Fourier recycling Averaged image Deconvoluted image

Original EM from Prof. N. Uyeda Symmetry averaging ED from Prof. N. Uyeda Original EM from Prof. N. Uyeda Two-Step Image Processing Image deconvolution Phase extension Fourier recycling Search for defocus Partial structure model Complete

Getting started Format: Image file (8-bit gray-level bitmap) HREM image (.bmp) Format: Image file (8-bit gray-level bitmap) Electron diffraction data (.dhk) Format: ASCII file Two modes are available to open this file Lattice parameters of the crystal Unit cell: a, b, c, , ,  Space group

Pre - processing Fourier filtering Symmetry averaging

Searching for focus value Experimental estimation (rough value): Minimum-contrast defocus: Focusing steps The rough defocus value for the image

Searching for focus value a set of trial f around the rough defocus value direct method by Sayre Equation: figures of merit (FOM) For Direct Methods, figures of merit are a measure of the quality of a given phase set. They characterize how well the phase set is satisfying the Sayre equation.

Image deconvolution Low-resolution structure restoration The resolution of the deconvoluted image is limited by the image resolution of the microscope.

Phase extension direct method by Sayre Equation: Program: SAPI for solving conventional and commensurate modulated structures (superstructures). Program: DIMS for 1D-incommensurate structures DIMS is based on the multidimensional direct methods

others modeling: Based on either a deconvoluted image or a resolution-enhanced image, a structure mode can be built. simulation: Dynamical ED and HREM simulation in VEC are available but still in a primary stage. A special feature of the simulation in VEC is that it can handle one-dimensionally modulated incommensurate crystals.

More others working with four-dimension (4D) structure: Commensurate modulated structure. Incommensurate modulated structure.

What’s a Modulated Structure ? T ¹ 0 (mod t) or MOD (T, t) ¹ 0 Incommensurate modulation Þ incommensurate structures t T T = 0 (mod t) or MOD (T, t) = 0 Commensurate modulation Þ superstructures

An example: Bi2(Sr0.9La0.1)2CoOy JEOL-2010, resolution ~ 2 Å

Schematic diffraction pattern of an incommensurate modulated structure b* q

Applications VEC has been successfully applied to structure determination of ten different crystals so far: Two commensurate modulated structure. Three incommensurate modulated structure. Five other conventional crystals. More ongoing cases….

Demo Now… But, don’t trust DEMO so much 