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"Resolving problems into solutions: - freely available crystallographic software for single crystal and powder diffraction"

by Lachlan M. D. Cranswick (CCP14 Project Secretary)

For presentation at the CNRS Laboratoire de Cristallographie, 25 rue des Martyrs, Grenoble, France; Thursday 2pm, 18th April 2002

Local contact: Pierre Bordet (English Version)

[CNRS Laboratoire de Cristallographie, Grenoble, France] | [(English Version)]

This page is located at http://www.ccp14.ac.uk/poster-talks/cnrs_2002/


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Table of Contents

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

Notes Free Zone

Aims of the UK EPSRC funded CCP14 Project

Talk Aims

For those new to Crystallography

Using the right crystallographic method can make the difference!

The risks of "not knowing what you don't know"

Why bother knowing about a variety of modern software? (1 of 2)

Why bother knowing about freely available software? (2 of 2)

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 Ė 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 directly into the structure databases

Powder Data Conversion / Importing Data

Structure Importing, Conversion and Transformation

Powder Sample Preparation and Data Collection

Variable Count Time data collection

VCT Literature References

VCT for trace Phase ID (1 of x) Fixed Count Time data (data collected by Jeremy Cockcroft)

VCT for trace Phase ID (1 of x) Variable Count Time data (displayed as FCT) (data collected by Jeremy Cockcroft)

VCT for trace Phase ID (1 of x) Fixed Count Time data (zoomed)

VCT for trace Phase ID (1 of x) Variable Count Time data (displayed as FCT)

Variable Count Time applications

VCT to aid in phase ID and profile fitting (1 of 2) Fixed Count Time

VCT to aid in phase ID and profile fitting (2 of 2) Variable Count Time

VCT for Structure Solution and Refinement (1 of 4) Variable Count Time data (as collected)

VCT for Structure Solution and Refinement (2 of 4) Variable Count Time data (displayed as FCT)

VCT for Structure Solution and Refinement (3 of 4) Variable Count Time data (displayed as FCT)

VCT for Structure Solution and Refinement (4 of 4) Variable Count Time data (displayed as VCT)

Where is VCT Data Collection?

Powder Diffraction Utility Software

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

Powder Indexing - a non trivial endeavour

Powder Indexing - the "Crysfire" suite

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

Chekcell : easy to see non-matching or impurity peaks

Chekcell : automatic cell and spacegroup searching

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

Chekcell: GUI Cell transformation

Chekcell: Density / Z / Molecular Volume Explorer

Chekcell: example of using Le Page

Crysfire / Chekcell: indexing powder Protein data

Why doesnít this powder sample index?

Some Alternatives to Crysfire: Winplotr, PowderX

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

ROTAX Single Crystal Twinning Software

"Generic" structure solution from powder diffraction data

"Specialised and Commercial" Structure Solution Programs

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

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

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

EXPO direct methods in action (4 of 4) Structure after being solved and auto built

Realspace programs for solving structures from powders

New FOX real space structure solution by Vincent Favre-Nicolin and Radovan Cerny

Adding polyhedra in Fox - 1 of 5

Adding polyhedra in Fox - 2 of 5

Adding polyhedra in Fox - 3 of 5

Adding polyhedra in Fox - 4 of 5

Adding polyhedra in Fox - 5 of 5

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 David Watkin, Richard Cooper, et al.: http://www.xtl.ox.ac.uk/

Guided structure refinement using Crystals

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 New validation via CCDC Mogul program: geometry checking

Validation using Crystals Cambridge database geometry check (2 of 3)

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

Graphs of HKL stats in Crystals

Structure Refinement using Powder Diffraction Data (Rietveld Refinement)

Rietveld Program Interfaces

Rietveld Programs - Rietica by Brett Hunter

Mentioning GSAS Rietveld: Some Relevant Background

GSAS : Solving and refining a protein from powder data

Brian Tobyís EXPGUI Interface for GSAS

Restrained Rietveld structure refinement of organics

Fourier capability in Rietveld Software

Single Crystal Suites (also applicable to powder diffraction)

WinGX for Windows single crystal suite Louis Farrugia: http://www.chem.gla.ac.uk/~louis/software/

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

WinGX for Windows single crystal suite Viewing the raw CCD frames and raw profile data

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 now links to Crystals as well)

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

Some Specialist Applications

Quantitative Phase Analysis

MAUD for Java : GPLíd (you get the source code)

Quantitative Phase Analysis - is it routinely easy?

Graphically interacting with the structure

Graphically interacting with the structure (more examples)

Platon: Validation - why taking an interest?

Structure validation and quality checking

WinGX for Windows single crystal suite Validation and Structure Checking

Platonís Addsym (by Ton Spek): checking for extra symmetry : e.g., 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 - finding extra symmetry in inorganics and minerals - P1 triclinic starting structure.

Platonís Addsym: for powders

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 GUI WinORTEP / GUI Struplo / WinGX

Photorealistic hardcopy output of structures Using GRETEP by Jean Laugier and Bernard Bochu

Photorealistic hardcopy output of structures Balls and Sticks - Polyhedral, etc

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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