A Brief Instruction to VEC A Brief Instruction to VEC

Hua Jiang

Free download with instructions Free download with instructions and examples atand examples at

http://cryst.iphy.ac.cn

Free download with instructions Free download with instructions and examples atand examples at

http://cryst.iphy.ac.cn

The big pictureThe big picture

Phases inside inner spherePhases inside inner sphere

Amplitudes inside two spheres

Amplitudes inside two spheres

Phases betweentwo spheres

Phases betweentwo spheres

Phase extension

Phase extension

Hie

DD

IHF

)(H

Hie

structurestructure

Deconvolution of a Single EMDeconvolution of a Single EM

far from the Scherzer defocus

far from the Scherzer defocus

Original image

Original image

Averaged image

Averaged image

Deconvoluted image

Deconvoluted image

Image after Fourier

recycling

Image after Fourier

recycling

Image of the final model

Image of the final model

Imagedeconvolution

Imagedeconvolution

Phase extension

Phase extension

FourierrecyclingFourier

recycling

Search for defocus Partial structure model

Partial structure model

Complete structure

model

Complete structure

model

Original EM from Prof. N. Uyeda

Original EM from Prof. N. Uyeda

Two-Step Image ProcessingTwo-Step Image ProcessingTwo-Step Image ProcessingTwo-Step Image Processing

SymmetryaveragingSymmetryaveraging

ED from Prof. N.

Uyeda

ED from Prof. N.

Uyeda

Getting startedGetting 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

Pre - processingPre - processing

• Fourier filtering

• Symmetry averaging

Searching for focus valueSearching for focus value

• Experimental estimation (rough value):

Minimum-contrast defocus:

Focusing steps

The rough defocus value for the image

04.0 21

min Csf

RCsf 21

rough 4.0

reading) instrument (from 0R

Searching for focus valueSearching 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.

h

hhhh FFV

F

Image deconvolutionImage deconvolution

• Low-resolution structure restoration

h

hh

W

TF

2

)(

The resolution of the deconvoluted image is limited by the image resolution of the microscope.

Phase extensionPhase extension

• direct method by Sayre Equation:

h

hhhh FFV

F

• Program: DIMS

• Program: SAPI

for solving conventional and commensurate modulated structures (superstructures).

for 1D-incommensurate structuresDIMS is based on the multidimensional direct methods

othersothers

• 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 othersMore others

• working with four-dimension (4D) structure:

Commensurate modulated structure.

Incommensurate modulated structure.

What’s a Modulated Structure ?What’s a Modulated Structure ?

tT

T = 0 (mod t) or MOD (T, t) Commensurate modulation

superstructures

T

T 0 (mod t) or MOD (T, t) Incommensurate modulation

incommensurate structures

TT

An example:An example:

JEOL-2010, resolution ~ 2 Å

BiBi22(Sr(Sr0.90.9LaLa0.10.1))22CoCoOOyyBiBi22(Sr(Sr0.90.9LaLa0.10.1))22CoCoOOyy

Schematic diffraction pattern

of an incommensurate modulated structure

Schematic diffraction pattern

of an incommensurate modulated structure

a*a*

b*b*qq

1 2 3* * *q q q q a b c1 1 2 2 3 4 43h h h h h bb b b

1 2 3 4

1 2 3 4

, , ,

( *,0), ( *,0), ( *,0), ( , )

h h h k h l h m b a b b b c b q d

* * *+h k l m h a b c q

Applications Applications

• VEC has been successfully applied to structure determination of ten different crystals ten different crystals so far:

Two commensurate modulated structure.

Three incommensurate modulated structure.

Five other conventional crystals.

More ongoing cases….

Demo Now…Demo Now…

But, don’t trust DEMO so much