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Queen Mary University of London, Wed 19th September 2001 - 11:00am Talk - Dissolving problems into solutions: freely available crystallographic software for single crystal and powder diffraction

by Lachlan M. D. Cranswick

Queen Mary University of London, Mile End Road, E1 4NS

(Talk contact: Rory Wilson (E-mail: r.m.wilson@mds.qmw.ac.uk)

This page is located at http://www.ccp14.ac.uk/poster-talks/qmul_2001/


Click here to start


Table of Contents

Dissolving problems into solutions: freely available crystallographic software for single crystal and powder diffraction.

Aims of the EPSRC funded CCP14 Project

Talk Aims

Notes Free Zone - they are on the web http://www.ccp14.ac.uk/poster-talks/qmul_2001/

For those new to Crystallography

Using the right crystallographic method can make the difference!

The risks of not knowing what you donít know

Why bother knowing about a variety of crystallographic software

Why bother knowing about a variety of modern software? (2 of 4)

Why bother knowing about a variety of modern software? (3 of 4) - Crystallographic Weaponry 101

Why bother knowing about freely available software? (4 of 4)

Single Crystal vs Powder diffraction (1 of 6)

Single Crystal vs Powder diffraction (2 of 6)

Single Crystal vs Powder diffraction (3 of 6)

Single Crystal vs Powder diffraction (4 of 6)

Single Crystal vs Powder diffraction (5 of 6)

Single Crystal vs Powder diffraction (6 of 6)

Talk Agenda

Phase Identification/Search Match for Powder Diffraction

Phase Identification/Search Match for Powder Diffraction 2 of 3 - Identifying an organic - DL-Valine

Phase Identification/Search Match for Powder Diffraction 3 of 3 - Multiphase mixture: Flourite, Corundum, Zincite

Has the structure been solved already? - Crystallographic Structure Databases

ICSD via the Web

A hopeful trend: Crystallography Suites that link into the structure databases

Powder Data Conversion / Importing Data

Structure Importing, Conversion and Transformation

Powder Diffraction Utility Software

Peak Profiling - (indexing, unit cell refinement, size/strain, etc)

Peak Profiling: Crystallite size and strain using Fundamental Parameters peak profiling in XFIT

Powder Indexing - a non trivial endeavour

Powder Indexing - the 'Crysfire' suite

Chekcell: Interpreting Crysfire Summary Files: - Powder Indexing and Spacegroup Assignment

Chekcell : automatic cell and spacegroup searching

Chekcell: 'integration' of Ton Spek and A. Meetsmaís Le Page

Chekcell: GUI Cell transformation

Chekcell: example of using Le Page

Crysfire / Chekcell: indexing powder Protein data

Why doesnít this powder sample index?

Unit Cell Refinement (powders)

CELREF for Unit Cell Refinement

Full Profile Fitting (Powder)

Le Bail full profile fitting - Rietica Rietveld

Le Bail full profile fitting - Rietica Rietveld - 2 of 2

Unit Cell Refinement: Mass Le Bail fitting: multi-phase - overlapping patterns

Materials Analysis Rietveld/Texture Software

Single Crystal Absorption Correction Options

Single Crystal Absorption Correction : WinGX

Platon options for absorption correction

Single Crystal Indexing / Twinning

'Generic' structure solution from powder diffraction data

'Specialised and Commercial' Structure Solution Programs

EXPO in Action (1 of 4) - Edit the input / control file

EXPO in action (2 of 4) - Click on the OK button to start

EXPO in action (3 of 4) - Le Bail fitting of the powder pattern

EXPO in action (4 of 4) - Structure after solved by direct methods

Single Crystal Structure Solution

Single Crystal Structure Solution - (Whatís it like to use the software?)

Shelxs direct methods - (tetracycline hydrochloride) via WinGX as an interface

Sir direct methods and auto Fourier building - (tetracycline hydrochloride) via WinGX as an interface

Dirdif Patterson methods and auto Fourier building - (tetracycline hydrochloride) via WinGX as an interface

Crunch for UNIX direct methods and Fourier building - (tetracycline hydrochloride) via Platon/System S as an interface

2D to 3D model building software

Getting fragments into Dirdif and Patsee for Windows

Single Crystal Structure Refinement Software - (Applicable to powder diffraction for helping build up the structure)

Example of Crystals for Windows

Guided structure refinement using Crystals

Guided structure refinement using Crystals

Guided structure refinement using Crystals - Have now refined atom positions Isotropically

Guided structure refinement using Crystals - Have now refined atom positions anisotropically

Guided structure refinement using Crystals - Automatic Hydrogen Addition

Interrupt the Guided Refinement in Crystals - Manual Hydrogen Addition - 1 of 2

Interrupt the Guided Refinement in Crystals - Manual Hydrogen Addition - 2 of 2

Interrupt the Guided Refinement in Crystals - Generating Fourier maps and Marching Cubes for Windows

Structure refinement using Crystals - Validation via Cambridge database: geometry checking

Validation using Crystals - Cambridge database geometry check (1 of 4)

Validation using Crystals - Cambridge database geometry check (2 of 4)

Validation using Crystals - Cambridge database geometry check (3 of 4)

Validation using Crystals - Cambridge database geometry check (4 of 4)

Structure Refinement using Powder Diffraction Data - (Rietveld Refinement)

Rietveld Program Interfaces

Mentioning GSAS Rietveld: Some Relevant Background

GSAS : Solving and refining a protein from powder data

GSAS: Individual Histogram Weighting

GSAS: Individual Histogram Weighting (use Sum(w*d**2) as a guide)

GSAS : Combined refinement on both XRD and Neutron

Rietveld: Rod Hill and Ian Madsen VCT data collection

Restrained Rietveld structure refinement of organics

Fourier capability in Rietveld Software

Single Crystal Suites - (applicable to powder diffraction)

WinGX for Windows single crystal suite

WinGX for Windows single crystal suite - Families of programs included/linkable with WinGX

WinGX for Windows single crystal suite - Absorption Correction

WinGX for Windows single crystal suite - Structure Solution

WinGX for Windows single crystal suite - Refinement - Shelxl 97

WinGX for Windows single crystal suite - Hydrogen Addition options

WinGX for Windows single crystal suite - Easy Interlinking with Ton Spekís Platon

WinGX for Windows single crystal suite - Fourier Electron Density Contour Maps

WinGX for Windows single crystal suite - Structure Plotting

WinGX for Windows single crystal suite - Validation and Structure Checking

Some Specialist Applications

Quantitative Phase Analysis

Quantitative Phase Analysis - pharmaceuticals

Graphically interacting with the structure

Graphically interacting with the structure - (more examples)

Crystal Structure validation - Why Bother?

Structure validation and quality checking

WinGX for Windows single crystal suite - Validation and Structure Checking

Platonís Addsym (by Ton Spek): - Structure Published in 1997 - P1 - Triclinic: 42 non-H atoms

Platonís Addsym: Correction Published in 1999: - C2 - Monoclinic: 22 non-H atoms

Platonís Addsym: Press of a button: 2000: - FDD2 - Orthorhombic: 11 non-H atoms

Platonís Addsym - (1 of 2) finding extra symmetry in inorganics and minerals - P1 triclinic starting structure.

Platonís Addsym - (2 of 2) finding extra symmetry in inorganics and minerals - P1 triclinic starting structure.

Powder diffraction pattern calculation - Powder Cell for Windows

Powder diffraction pattern calculation - Poudrix for Windows

Photorealistic hardcopy output of structures

Photorealistic hardcopy output of structures - Ortep-3 / GUI Struplo / WinGX

Photorealistic hardcopy output of Fourier Maps - Marching Cubes by Michal Husak

Dual Boot UNIX / Windows PC and Crystallographic Nexus CD-ROMs for those isolated from the internet

Summary

Author: Lachlan M. D. Cranswick

Email: l.m.d.cranswick@dl.ac.uk

Home Page: http://www.ccp14.ac.uk

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