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A Brief Instruction to VEC

A Brief Instruction to VEC. Hua Jiang. Free download with instructions and examples at http://cryst.iphy.ac.cn. Phase extension. d I. d I. Phases between two spheres. structure. d. D. The big picture. Amplitudes inside two spheres. Phases inside inner sphere. Original image.

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A Brief Instruction to VEC

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

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

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

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

  5. Getting started • 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

  6. Pre - processing • Fourier filtering • Symmetry averaging

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

  8. 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.

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

  10. 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

  11. 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.

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

  13. T T T T t T = 0 (mod t) or MOD (T, t) = 0 Commensurate modulation Þ superstructures T¹ 0 (mod t) or MOD (T, t) ¹ 0 Incommensurate modulation Þ incommensurate structures What’s a Modulated Structure ?

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

  15. b* q a* Schematic diffraction pattern of an incommensurate modulated structure

  16. 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….

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

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