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ACA 2001 Talk - Building a teaching course around crystallographic freeware

by Lachlan M. D. Cranswick

For ACA 2001 - Los Angelos, USA: 21st July to 26th July 2001

This page is located at http://www.ccp14.ac.uk/poster-talks/aca2001/


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Table of Contents

Building a teaching course around crystallographic freeware

Main aim of this talk

Notes Free Zone - they are on the web - http://www.ccp14.ac.uk/poster-talks/aca2001/

Why bother considering a variety of modern software? (1 of 4)

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

Why bother using and teaching a variety of modern software? (3 of 4) - Crystallographic Weaponry 101

Why bother using freely available software? (4 of 4)

Agenda for Some Examples

Hopefully Platon / System S demonstration worked! - (Ton Spek - http://www.cryst.chem.uu.nl/platon/)

Platon / System S for UNIX / Linux / FreeBSD - (Ton Spek - http://www.cryst.chem.uu.nl/platon/)

Gretep structure plotting / symmetry - (by Jean Laugier and Bernard Bochu) - (http://www.ccp14.ac.uk/tutorial/lmgp/)

Gretep: Showing symmetry operators (1)

Gretep: Showing symmetry operators (2)

Gretep: Each fragment with a different colour

If time limited: more chance to get your points across to students if examples are interactive

Scatfac for interactively investigating scattering factors (http://www.ccp14.ac.uk/tutorial/lmgp/)

Dispano for Anomalous Scattering factor display (http://www.ccp14.ac.uk/tutorial/lmgp/)

Dispano for Anomalous Scattering factor display (http://www.ccp14.ac.uk/tutorial/lmgp/)

Poudrix powder pattern calculation - With Anomalous Dispersion - (Brenann and Cowan or Sasaki) - (http://www.ccp14.ac.uk/tutorial/lmgp/)

PowderCell powder pattern calculation - (by Werner Kraus and Gert Nolze) - (http://www.ccp14.ac.uk/tutorial/powdcell/)

PowderCell - interactively moving atoms (1 of 3) - (http://www.ccp14.ac.uk/tutorial/powdcell/)

PowderCell - interactively moving atoms (2 of 3) - (http://www.ccp14.ac.uk/tutorial/powdcell/)

PowderCell - interactively moving atoms (3 of 3) - (http://www.ccp14.ac.uk/tutorial/powdcell/)

XFIT Peak Profiling - by Alan Coelho and Bob Cheary - (http://www.ccp14.ac.uk/tutorial/xfit-95/)

XFIT Peak Profiling - 1 of 4 - Load Data

XFIT Peak Profiling - 2 of 4 - Zoom up

XFIT Peak Profiling - 3 of 4 - Insert Peaks

XFIT Peak Profiling - 4 of 4 - Fit Peaks (auto-Marquardt damping)

Crysfire Powder Indexing - Robin Shirley (http://www.ccp14.ac.uk/tutorial/crys/)

Chekcell GUI indexing helper - Laugier & Bouchu (http://www.ccp14.ac.uk/tutorial/lmgp/)

Chekcell - Systematic Absences and space group possibilities - Laugier & Bouchu (http://www.ccp14.ac.uk/tutorial/lmgp/)

Chekcell - Systematic Absences - Scrolling down the spacegroups C2/M (1 of 5)

Chekcell - Systematic Absences - Scrolling down the spacegroups P2/C (2 of 5)

Chekcell - Systematic Absences - Scrolling down the spacegroups C2/C (3 of 5)

Chekcell - Systematic Absences - Scrolling down the spacegroups I2/C (4 of 5)

Chekcell - Systematic Absences - Scrolling down the spacegroups P21/A (5 of 5)

Chekcell - Systematic Absences - conditions for P21/A within Chekcell

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 - 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 Spek’s 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

Crystals for Windows single crystal suite - David Watkin, Richard Cooper, et al.: http://www.xtl.ox.ac.uk/

Guided structure refinement using Crystals - Import Shelx INS file of structure solved by DIRDIF

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

Guided structure refinement using Crystals - Checking Extinction

Guided structure refinement using Crystals - Optimize weights

Guided structure refinement using Crystals - Validate Structure

Guided 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)

Validation: Platon for UNIX and Windows - Ton Spek: http://www.cryst.chem.uu.nl/platon/

Platon: Validation - Why Bother teaching this?

Platon’s Addsym: Structure Published in 1997 - P1 - Triclinic: 42 non-H atoms

Platon’s Addsym: Correction Published in 1999: - C2 - Monoclinic: 22 non-H atoms

Platon’s Addsym: Press of a button: 2000: - FDD2 - Orthorhombic: 11 non-H atoms - (Short Communication Abstract: "P1 or P-1? Corrigendum", Acta Cryst B56 (2000) 744 from Richard E. Marsh)

Bonus Personal Rant: Need for the teaching of competent computer and OS skills!

Things to consider: Adding Computer skills and Programming to teaching courses.

Summary

 Author: Lachlan Cranswick - Geochemistry - Lamont-Doherty Earth Observatory of Columbia University, New York, USA

Email: lachlan@ldeo.columbia.edu

Home Page: http://www.ccp14.ac.uk/poster-talks/aca2001/

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