1. Freely available crystallographic software for powder diffraction.
L. M. D. Cranswick,
CCP14 (Collaborative Computation Project No 14 for
Single Crystal and Powder Diffraction)
Department of Crystallography;
Birkbeck College, University of London,
Malet Street, Bloomsbury, London, WC1E 7HX, UK.
WWW:

2. Notes Free Zone - they are on the web http://www. ccp14. ac
Some areas of this talk may resemble a rather fast computer slide show; thus detailed notes are on the web for examination at your leisure (and given out during the talk)
Slide 2
Lachlan M. D. Cranswick

3. Talk Aims
Show there is a variety of freely available software out there that can help you with your research via diffraction and crystallographic methods
Making use of the latest software can make your difficult problems easier or doable.
Slide 3
Lachlan M. D. Cranswick

4. For those new to Crystallography
Why bother looking into freely available crystallographic software?
Crystallography can help answer questions that may not seem very crystallographic at the time.
In the following screen images, help determine, using diffraction techniques, whether there is Oxygen in the Earth’s outer core. (unit cell volumes to obtain equations of state - EOS)
“O2 volumes at high pressure from KClO4 decomposition: D" as a siderophile element pump instead of a lid on the core.” D. Walker, S.M. Clark, L.M.D. Cranswick, M.C. Johnson and R.L. Jones, (2002), Geochemistry, Geophysics, Geosystems (G^3), in press.
Slide 4
Lachlan M. D. Cranswick

5. Using the right crystallographic method can make the difference!
Using Traditional UNIT CELL refinement Methods
Using Le Bail fitting / Rietveld
Slide 5
Lachlan M. D. Cranswick

6. The risks of “not knowing what you don’t know”
Thus this talk will try and get the keywords out that you can follow-up on at your leisure.
Slide 6
Lachlan M. D. Cranswick

7. Path of Most Resistance?
Why bother knowing about a variety of modern software? (1 of 2)
Path of Most Resistance?
Using a variety of “state-of-the-art” tools can improve versatility by allowing different pathways and approaches to tackle crystallographic problems.
Maximise the ability to handle present and future problems
Be able to cross hurdles that may be intractable or unnecessarily problematic if not approached the right way.
Slide 7
Lachlan M. D. Cranswick

8. Why bother knowing about freely available software? (2 of 2)
Much freely available software is state of the art in both algorithms and usability - (GUIs)
Concentrate on the crystallography
Can be installed on as many computers as you want - where-ever you like
Can take programs home and use on their personal computers (negate software piracy problems)
Slide 8
Lachlan M. D. Cranswick

9. Single Crystal vs Powder diffraction (1 of 9)
“Mass transit” structure solution and refinement
There are difficulties:
Crystal not representative of the bulk
Twinning
Crystal decomposes during data collection
“Difficult” structure
Slide 9
Lachlan M. D. Cranswick

10. Single Crystal vs Powder diffraction (2 of 9)
Cambridge Database
“During 1999, 17,898 new entries were added”
(that Scale is in the 100’s of thousands)
1999 report:
Slide 10
Lachlan M. D. Cranswick

11. Single Crystal vs Powder diffraction (3 of 9)
ICSD Database (inorganics - and minerals)
During first 6 months of 2002, 3073 new entries were added.
July 2002 ICSD release : a total of 64,848 entries
Slide 11
Lachlan M. D. Cranswick

12. Single Crystal vs Powder diffraction (4 of 9)
Powder Methods for solving structures
A nightmare to some
An adventure to others!
Slide 12
Lachlan M. D. Cranswick

13. Single Crystal vs Powder diffraction (5 of 9)
Number of structures solved by powder methods
592 up to end of 2001
Slide 13
Lachlan M. D. Cranswick

14. Single Crystal vs Powder diffraction (6 of 9)
Structure Determination from Powder Diffractometry Round Robin 1
Tetracycline Hydrochloride (June 1998)
Armel Le Bail and Lachlan Cranswick
Powder Data:
6 week time limit
70 downloads of data
2 submissions on the Tetracycline within the time limit
CSD System from Stoe
Druid/Mystic (now called Dash)
(also solved by Armel Le Bail)
Slide 14
Lachlan M. D. Cranswick

15. Single Crystal vs Powder diffraction (7 of 9)
Tetracycline structures obtained from microcrystal - single crystal diffraction : synchrotron X-rays
a powder can be a collection of very small single crystals
10x20x30 micron crystal (Clegg and Teat)
Beamline 9.8 at Daresbury Synchrotron: Bruker Smart CCD
Routine structure solution - including hydrogens found from the map
Solved at the press of a button as the data was being collected. (few hours data collection)
Slide 15
Lachlan M. D. Cranswick

16. Single Crystal vs Powder diffraction (8 of 9)
What about the “inorganic unknown” in the SDPD Round Robin?
No-one bothered to solve it (except Armel Le Bail)
One participant who solved the organic said the inorganic was “too boring” and thus did not try it.
Big fad at present is to solve organic pharmaceuticals from powders
Much commercial software development reflects this emphasis on pharmaceuticals
Slide 16
Lachlan M. D. Cranswick

17. Single Crystal vs Powder diffraction (9 of 9)
2nd SDPDRR (Indexing and solving):
Round robin started on Monday 9th September
Structure solution ending on Sunday 17th November
Slide 17
Lachlan M. D. Cranswick

18. Talk Agenda
Start from Data conversion and phase identification
Go through to photo realistically rendering crystal structures
Via stops including
Peak profiling
Unit Cell refinement
Powder indexing
Structure Solution
Structure refinement
Structure validation
Photorealistic rendering of crystal structures
Slide 18
Lachlan M. D. Cranswick

19. Phase Identification/Search Match for Powder Diffraction
Two main parts to perform computer based search-match:
1. Have a Powder Diffraction Database (buy or make your own)
2. Search-match software that uses the above database to search
Databases:
ICDD has the commercial powder diffraction database area cornered
Alternative being developed is the Pauling File:
Editor in Chief: Dr Pierre Villars
Nearly all Search-match programs are commercial:
Refer to, "Available Search-Match Software" for a list of known software:
Free Software:Brian Toby's "Portable Logic Program" (UNIX) and "MacDiff" for Apple Mac freeware by Rainer Petschick
Look out for the developing OpenXRD by Stefan Krumm (UNIX and Windows)
Slide 19
Lachlan M. D. Cranswick

20. Phase Identification/Search Match for Powder Diffraction 2 of 3 Identifying an organic – DL-Valine
Slide 20
Lachlan M. D. Cranswick

21. Which software, databases and methods work the best: Search Match Round Robin (2nd May 2002 to 30th June 2002): and CCP14 mirrors
Conclusions :
Search-match without chemistry is possible but:
Need up to date database
Need good 3rd generation search-match software
Need a skilled analyst
(the skilled analyst seems to be the most important of the 3)
Slide 21
Lachlan M. D. Cranswick

22. Has the structure been solved already
Has the structure been solved already? Crystallographic Structure Databases
(UK based academics and students already have free access via the EPSRC funded CDS (Chemical Database Service):
ICSD (Minerals and Inorganics)
Web accessible demonstration:
MDF/CRYSTMET
(Metals and Alloys)
CCSD
(Organics and Organometallics)
American Mineralogist
WWW Mincryst
2398 unique phases - most with crystal structure data
Mineral web
Slide 22
Lachlan M. D. Cranswick

23. ICSD via the Web
Using an Interface created by Alan Hewat at ILL, Grenoble, France
There is a trend for databases to use the web due to the convenience and effectiveness. Also has advantage of being operating system independent for users.
Slide 23
Lachlan M. D. Cranswick

24. A hopeful trend: Crystallography Suites that link directly into the crystal structure databases
Platon for UNIX (if CSD/Quest is also installed):
CSD Cell searching at the click of a button
Connectivity search: using the CORINA to generate a PDB file,
Then use Platon/System S acting as a friendly interface for Quest.
Slide 24
Lachlan M. D. Cranswick

25. Powder Data Conversion / Importing Data
Initial problem in powder diffraction can be getting the data in the right format. For interconverting powder diffraction data: a variety of programs exist which in combination can pretty much get you from one format to another
Summary list of available software:
Text Editors may occassionally be required: converting UNIX ACSII to DOS ASCII, getting rid of spaces or tabs , column editing:
Freeware PFE Editor for Windows:
Freeware ConTEXT Editor for Windows (does column editing)
Example of ConvX for Windows by Mark Bowden
Mass data powder diffraction data converter
Slide 25
Lachlan M. D. Cranswick

26. Structure Importing, Conversion and Transformation
Summary list of available software at:
Be careful to check the results
Best program for the moment is the shareware Cryscon
Other software such as GUI WinORTEP can import a wide variety of file formats and export these into Shelx format.
Example of Cryscon for Windows by Eric Dowty
Slide 26
Lachlan M. D. Cranswick

27. Powder Sample Preparation and Data Collection
Assumption is that you know about appropriate sample preparation and data collection
However, many hardware vendors might not provide the required flexibility in data collection
Slide 27
Lachlan M. D. Cranswick

28. Variable Count Time data collection
Main idea here is to increase the raw intensity of selected peak areas to assist in the “required” analysis: (similar to what a CAD4 does)
Up till now, if at all, mainly done for refinement (e.g., Hill and Madsen method)
On point detector (e.g., Bragg Bretano flat plate system), do this by varying the count time in a pre-defined manner
(Can also provide more time effective counting time)
Fixed Count Time
Variable Count Time
Slide 28
Lachlan M. D. Cranswick

29. VCT Literature References
"Collection and analysis of powder diffraction data with near-constant counting statistics", I. C. Madsen and R. J. Hill, J. Appl. Cryst. (1994). 27,
Philips Friendly Fortran source code that does this Hill and Madsen method is at:
(Original Hill and Madsen VCT (variable count time) Paper), I. C. Madsen and R. J. Hill, Adv. X-ray Anal. (1992), 35, 39-47
W. I. F. David, Accuracy in Powder Diffraction, Abstract P2.6 NIST Special Publication No. 846, Page 210, (1992) National Institute of Standards and Technology, Gaithersburg, MD, USA.
Slide 29
Lachlan M. D. Cranswick

30. VCT for trace Phase ID (1 of x) Fixed Count Time data (data collected by Jeremy Cockcroft)
Slide 30
Lachlan M. D. Cranswick

31. VCT for trace Phase ID (1 of x) Variable Count Time data (displayed as FCT) (data collected by Jeremy Cockcroft)
Slide 31
Lachlan M. D. Cranswick

32. VCT for trace Phase ID (1 of x) Fixed Count Time data (zoomed)
Slide 32
Lachlan M. D. Cranswick

33. VCT for trace Phase ID (1 of x) Variable Count Time data (displayed as FCT)
Slide 33
Lachlan M. D. Cranswick

34. Variable Count Time applications
Equally relevant to problems where you need to adequately profile fit small / trace peaks which might not be significantly above background in a “routine”, time effective fixed count time data collection - e.g.,;
Powder Indexing
Unit Cell refinement
Quantitative Rietveld Analysis
Slide 34
Lachlan M. D. Cranswick

35. VCT to aid in phase ID and profile fitting (1 of 2) Fixed Count Time
Slide 35
Lachlan M. D. Cranswick

36. VCT to aid in phase ID and profile fitting (2 of 2) Variable Count Time
Slide 36
Lachlan M. D. Cranswick

37. VCT for Structure Solution and Refinement (1 of 4) Variable Count Time data (as collected)
Slide 37
Lachlan M. D. Cranswick

38. VCT for Structure Solution and Refinement (2 of 4) Variable Count Time data (displayed as FCT)
Slide 38
Lachlan M. D. Cranswick

39. VCT for Structure Solution and Refinement (3 of 4) Variable Count Time data (displayed as FCT)
Slide 39
Lachlan M. D. Cranswick

40. VCT for Structure Solution and Refinement (4 of 4) Variable Count Time data (displayed as VCT)
Slide 40
Lachlan M. D. Cranswick

41. Where is VCT Data Collection?
Not a routine or available option in commercial XRD control software
Something to keep an eye on - or request from vendors.
Is in the new Bede powder diffraction system
Slide 41
Lachlan M. D. Cranswick

42. Powder Diffraction Utility Software
Examining Data, peak finding, background stripping, alpha-2 stripping
Powder v 2.00:
Powder X,
WinFIT,
Winplotr,
XFIT,
Example of PowderX for Windows
Graphical evaluation, backtground stripping, smoothing, alpha stripping, peak find and pass to treor indexing
Full GUI Operation
Powder X
(Alpha2 Strip, Background Strip, Peak Find)
Slide 42
Lachlan M. D. Cranswick

43. Peak Profiling (indexing, unit cell refinement, size/strain, etc)
For Overall Summary of available peak profiling software refer to:
These include: CMPR, DRXWin, EFLECH, GPLSFT, pearson.xls, SHADOW, Powder v2.00, PowderX, Winfit, Winplotr, XFIT
Examples of XFIT for Windows
Slide 43
Lachlan M. D. Cranswick

44. Powder Indexing - a non trivial endeavour
For Overall Summary of available powder indexing software refer to:
Powder Indexing: Autox, Ito, Dicvol, Treor, Taup/Powder, Lzon, Losh, Kohl, Scanix, Xrayscan, EFLECH/Index, Supercell
Linking Suites: Crysfire, Powder v2.00, PowderX, PROSZKI, WinPlotr, Chekcell
supercel is a specialise indexing program by Juan Rodriguez-Carvajal for indexing Super Cell and Incommensurate cells. (available within Winplotr)
ftp://bali.saclay.cea.fr/pub/divers/fullprof.2k/
Slide 44
Lachlan M. D. Cranswick

45. Powder Indexing - the “Crysfire” suite
At present the CRYSFIRE software by Robin Shirley links 8 different indexing programs (ito, dicvol, treor, taup, kohl, lzon, fjzn and losh) together with a common interface and using intelligent defaults. Important to have access to as many indexing programs as possible so you can get a feel for the range of possible solutions.
Example of CRYSFIRE Screen prompting the saving into one of 8 different indexing program formats:
Slide 45
Lachlan M. D. Cranswick

46. Chekcell: Interpreting Crysfire Summary Files: Powder Indexing and Spacegroup Assignment
Crysfire interlinks with Chekcell for Windows (part of the LMGP suite for Windows by Jean Laugier and Bernard Bochu). Chekcell provides a graphical interface for manually and automatically suggesting a best cell/spacegroup combination using both FOM and algorithms relating to parsimony of superfluous HKLs.
Slide 46
Lachlan M. D. Cranswick

47. Chekcell : automatic cell and spacegroup searching
can trudge through a single selected unitcell; or over 1000s of trial cells looking for the best cell and spacegroup combination based on “parsimony of extra reflections” criteria.
Slide 47
Lachlan M. D. Cranswick

48. Chekcell: “integration” of Ton Spek and A. Meetsma’s Le Page
Obtaining the Reduced Cell
which many powder indexing programs to not reliably determined
Refer: "'Reduced Cells', M.J. Buerger, (Zeitschift fur Kristallographie, BD 109, S (1957)”
Efficient Sub-cell and super-cell searching, then easy reviewing of newly derived cells within the Chekcell interface
Slide 48
Lachlan M. D. Cranswick

49. Chekcell: example of using Le Page
Orthorhombic cell with good FOM (Figure of Merit)
Le Page combined with automatic “Best Solution” easily finds a better hexagonal cell based on parsimony of extra reflections criteria
Slide 49
Lachlan M. D. Cranswick

50. Crysfire / Chekcell: indexing powder Protein data
Using the “Rescale” feature in Crysfire
Finds the correct rhombohedral cell as published in:
R. B. Von Dreele, P. W. Stephens, G. D. Smith and R. H. Blessing, "The first protein crystal structure determined from high-resolution X-ray powder diffraction data: a variant of T3R3 human insulin-zinc complex produced by grinding", Acta Cryst. (2000). D56,
Slide 50
Lachlan M. D. Cranswick

51. Some Alternatives to Crysfire: Winplotr, PowderX
Winplotr by Juan Rodriguez-Carvajal
PowderX by Cheng Dong
Powder v2 by Nita Dragoe
CMPR for Windows and UNIX by Brian Toby
Slide 51
Lachlan M. D. Cranswick

52. New MCMaille by Armel Le Bail (Sep 2002)
Monte Carlo Cell finding / indexing software
Whole Profile method using reconstituted peaks positions and intensities
Not sensitive to trace impurities
Poor data can still give no reasonable result.
Slide 52
Lachlan M. D. Cranswick

53. Unit Cell Refinement (powders)
For Overall Summary of available unit cell refinement software refer to:
This includes:
Celref, LAPOD, Refcel, Unitcell, Eracel, Powder v2.00, XLAT, etc
Can be helpful to perform a conventional unit-cell refinement prior to a Le Bail fit (or where unit weighting of each reflection is important).
Slide 53
Lachlan M. D. Cranswick

54. CELREF for Unit Cell Refinement
by Jean Laugier and Bernard Bochu
In this example, celref is performing graphical Unit Cell refinement on calcite in a multi-phase mixture
Knows about spacegroups
Graphics can really help sort out errors or misassigned
Slide 54
Lachlan M. D. Cranswick

55. Full Profile Fitting (Powder)
For Overall Summary of available full profile analysis refer to:
Le Bail based:
Pawley Based:
The most common method of full profile fitting is that of Le Bail fitting: which is in most Rietveld packages. It is useful for:
Spacegroup Assignment
Unit Cell Refinement (especially when overlap is a problem)
Extracting Intensities for Structure Solution
Slide 55
Lachlan M. D. Cranswick

56. Le Bail full profile fitting - Rietica Rietveld
By Brett Hunter
Easy to use and setup via GUI
Le Bail is Structureless whole profile fitting - just need cell and spacegroup
Easy to add and delete structures
Auto-marquardt damping for initial unstable refinement if required
Slide 56
Lachlan M. D. Cranswick

57. Le Bail full profile fitting - Rietica Rietveld - 2 of 2
In this example multiphase system where the aim is to get accurate unit cell volumes.
No completely freestanding peak for KCl
Slide 57
Lachlan M. D. Cranswick

58. Unit Cell Refinement: Mass Le Bail fitting: multi-phase - overlapping patterns
Using Le Bail fitting
Using Traditional Methods
Slide 58
Lachlan M. D. Cranswick

59. Materials Analysis Rietveld/Texture Software
Pole Figure, Texture Analysis – important also for some forms of Le Bail fitting and structure solution from powders
Summary List of available software:
BEARTEX for Windows
GSAS Rietveld (Windows/UNIX)
MAUD for Java
POFINT
popLA
Symmet for DOS
TexturePlus for Windows
MAUD (for Java PC/Mac/UNIX)
Crystallite size and shape analysis
Slide 59
Lachlan M. D. Cranswick

60. “Generic” structure solution from powder diffraction data
Very non-trivial endeavour.
(though indexing can often be the limiting step in many attempted structure solutions)
EXPO - Direct Methods (Sirware Group) Makers of Sir92/Sir97/Sirpow
If EXPO fails, it is possible to use Le Bail or Pawley extracted data with Single Crystal Structure Solution Software as described in following slides.
Then consider real space methods such as using ESPOIR (GPL’d by Armel Le bail) or FOX (GPL’d by Vincent Favre-Nicolin and Radovan Cerny) - normally real space methods use as last resort:
ESPOIR: sdpd.univ-lemans.fr /sdpd/espoir/
Web tutorial on setting up the ESPOIR files in < 10 minutes" and example of solving on an organic molecule:
FOX:
Slide 60
Lachlan M. D. Cranswick

61. “Specialised and Commercial” Structure Solution Programs
PSSP – molecular structures
ZEFSA II – for Zeolites (GPL’d)
Focus – for Zeolites
Fullprof – Monte Carlo for structure solution and finding Magnetic Moments in neutron data
ftp://bali.saclay.cea.fr/pub/divers/winplotr/
“Available” Commercial Structure Solution from Powder Diffraction Data software:
Powder Solve:
Crystal Structure Determination Package (WinCSD/CSD) :
DASH (Druid and Mystic of old):
TOPAS :
Endeavour :
Slide 61
Lachlan M. D. Cranswick

62. EXPO direct methods in Action (1 of 4) Edit the input / control file
Slide 62
Lachlan M. D. Cranswick

63. EXPO direct methods in action (2 of 4) Click on the OK button to start
Slide 63
Lachlan M. D. Cranswick

64. EXPO direct methods in action (3 of 4) Le Bail fitting of the powder pattern
Slide 64
Lachlan M. D. Cranswick

65. EXPO direct methods in action (4 of 4) Structure after being solved and auto built
Slide 65
Lachlan M. D. Cranswick

66. New FOX real space structure solution by Vincent Favre-Nicolin and Radovan Cerny
Available for UNIX/Linux and MS-Windows
GUI Based
Very user friendly in setting up rigid bodies
Includes automatic merging of atoms on special position with dynamic occupancy correction
Slide 66
Lachlan M. D. Cranswick

67. Adding polyhedra in Fox - 1 of 5
Click on “Crystals”, “Scatterers” Icon, “Add”
Slide 67
Lachlan M. D. Cranswick

68. Adding polyhedra in Fox - 2 of 5
Select the central atom
Slide 68
Lachlan M. D. Cranswick

69. Adding polyhedra in Fox - 3 of 5
Select the corner atom(s)
Slide 69
Lachlan M. D. Cranswick

70. Adding polyhedra in Fox - 4 of 5
Give the Bond length
Slide 70
Lachlan M. D. Cranswick

71. Adding polyhedra in Fox - 5 of 5
Done!
Slide 71
Lachlan M. D. Cranswick

72. Single Crystal Structure Solution
Applicable to powder diffraction:
CAOS (also inside part of Sir97) – Ricardo Spagna, et. al.
Patterson Solution Option.
Crisp – Part of the GPL’d Xtal Suite
Direct Methods
Crunch – R. de Gelder, R.A.G. de Graaff & H. Schenk,
Direct Methods and automatic structure building
Dirdif - P.T. Beurskens, G. Beurskens, R. de Gelder, et al. - UNIX and Windows
Patterson Methods for heavy atoms and fragments and automatic structure building
Patsee – E. Egert and G. Sheldrick
Fragment Search
SAPI and DIMS – Fan Hai-Fu, et al.
Direct methods including ability to handle pseudo-symmetry and incommensurate modulated structures and composite structures (Windows)
Shake’n’Bake (SnB) – Weeks, Miller, et al.
Dual-space direct methods. (Linux, SGI, IBM AIX, Alpha executables via web)
ShakePSD/DS*SYSTEM – Kenji Okada
Windows based direct methods for large structures up to 500 atoms
Shelxs 86/97/d- George Sheldrick
Direct Methods and Patterson Option
Sir92/97/2000 – Sirware Group: Cascarano, Giacovazzo el al
Solver – in NRCVAX Suite – based on Multan
Slide 72
Lachlan M. D. Cranswick

73. 2D to 3D model building software
Applicable for Generating 3D fragments for Patsee/Dirdif Orient – single crystal/powder
Summary list at:
E.g., CORINA (COoRdINAtes) (Use web based direct submission):
Comes with a Java Molecule Editor for building up the 2D structure over the web which generates the required SMILES string from the drawn molecule. In this example a 2D tetracyline PDB file is generated: CN(C)C3C(O)=C(C(N)=O)C(O)C4(C)C(O)C2C(=O)c1c(O)cccc1C(C)(O)C2CC34
(Word of warning: the “energy minisation” may generate an inaccurate 3D model where different conformations are possible)
Slide 73
Lachlan M. D. Cranswick

74. Getting fragments into Dirdif, Patsee for Windows
One of the User Friendliest methods is to use is WinGX’s “SXGRAPH” GUI Shelx INS/RES file Editor
Either graphically Browse and Edit the Orbase Entries or Open an imported structure file (CSSR, CSD, Shelx or CIF from existing structure refinement), clean it up, then save it as a fragment ready for immediate use with Dirdif for Windows. (or any Dirdif)
For Dirdif: File, Save ATMOD File
For Patsee: File, Save PATSEE File
Slide 74
Lachlan M. D. Cranswick

75. Single Crystal Structure Refinement Software (Applicable to powder diffraction for helping build up the structure)
Range of programs to choose from:
CAOS (also inside Sir97)
Crystals
DS*SYSTEM/LSBF
Jana
NRCVAX
Shelxl
(Shelxl is within 3 freely available crystallographic suites)
WinGX
Platon/System S
ORTEX
Xtal (GPL’d)
Slide 75
Lachlan M. D. Cranswick

76. Example of Crystals for Windows David Watkin, Richard Cooper, et al
Will focus on Hydrogen addition
Import the structure from Shelx or Sir
Assymetric unit is always in view
Bond types are graphically displayed for instant feedback.
Slide 76
Lachlan M. D. Cranswick

77. Guided structure refinement using Crystals
Automatic Hydrogen Addition
Slide 77
Lachlan M. D. Cranswick

78. Interrupt the Guided Refinement in Crystals Manual Hydrogen Addition - 1 of 2
Crystals explains what is going on in a language organic chemists and students can understand
Slide 78
Lachlan M. D. Cranswick

79. Interrupt the Guided Refinement in Crystals Manual Hydrogen Addition - 2 of 2
A “Wizard” then guides the user to complete the hydrogen addition
Slide 79
Lachlan M. D. Cranswick

80. Structure refinement using Crystals New validation via CCDC Mogul program: local geometry checking
To students and new users, every structure must seem like a new structure type. Thus using Mogul geometry check can encourage students to look for errors or novel features of the structure.
Slide 80
Lachlan M. D. Cranswick

81. Validation using Crystals Cambridge database local geometry check (2 of 2) Mogul is spawned and gives distributions of bond lengths and angles
Slide 81
Lachlan M. D. Cranswick

82. Validation within Rietveld / powder Software
Normally done manually or by linking into other software: such as Platon (EXPGUI links to Platon)
However various Rietveld programs links to some options:
Following example of “Bond - Valence” calculations within Rietica
Slide 82
Lachlan M. D. Cranswick

83. Structure Refinement using Powder Diffraction Data (Rietveld Refinement)
Large range of programs to choose from:
Many specialize for particular types of problems, incommensurate structures, quantitative analysis, polymers, etc.
ARITVE, BGMN, DBWS, DEBVIN, EXPO
Fullprof, GSAS, Koalariet, LHPM-Rietica, MAUD for Java (GPL’d)
Premos/Remos, ProDD, Profil, Riet7/SR5, Rietan 2000 (GPL’d)
Rietquan, Simref, WinMprof, XND, XRS-82/DLS-76
Slide 83
Lachlan M. D. Cranswick

84. Rietveld Program Interfaces
Not yet as robust and powerful as single crystal refinement programs (Single Crystal programs are very poweful and do a lot for the user)
Unlike most single crystal suites, you are not interacting directory with the structures on the screen.
Many choose their Rietveld based on what the people down the road are using. Not only human nature but learning a Rietveld program from scratch can be difficult.
Interfaces into Rietveld programs vary from GUIs to direct editing of ASCII files.
Slide 84
Lachlan M. D. Cranswick

85. Rietveld Programs - Rietica by Brett Hunter
Full Graphical User Interface
Still got to appreciate and know your crystallographyfor inserting and refining the crystal structure
Slide 85
Lachlan M. D. Cranswick

86. Mentioning GSAS Rietveld: Some Relevant Background
by Bob von Dreele and Alan Larsen
Menu based control
Available for Windows / DOS / Linux / SGI
Separate GUI by Brian Toby (EXPGUI)
Combined X-ray / Neutron / Single Crystal / Powder Diffraction
Integrated Fourier map generation and viewing
GSAS resources, tutorials and links (including links to EXPGUI)
Restraints
Bond angle
Bond length
Planar
Total Chemistry / charge balance
Chiral volume
Phi/psi group
Torsion angle
Manual Marquadt damping
Atom shift limits
Lots of other features
Slide 86
Lachlan M. D. Cranswick

87. GSAS : Solving and refining a protein from powder data
As cited in R. B. Von Dreele, P. W. Stephens, G. D. Smith and R. H. Blessing, "The first protein crystal structure determined from high-resolution X-ray powder diffraction data: a variant of T3R3 human insulin-zinc complex produced by grinding", Acta Cryst. (2000). D56,
Slide 87
Lachlan M. D. Cranswick

88. Brian Toby’s EXPGUI Interface for GSAS
User friendlier to start using GSAS via EXPGUI
(A new combined installer makes it very easy to start using GSAS.)
Slide 88
Lachlan M. D. Cranswick

89. Restrained Rietveld structure refinement of organics
Software not as powerful as single crystal but there are some tutorials with tricks on the CCP14 website
Slide 89
Lachlan M. D. Cranswick

90. Fourier capability in Rietveld Software
GSAS
(including VRML output)
Fullprof /
GFOUR for Windows
Summary list of Fourier friendly Rietveld software at:
Slide 90
Lachlan M. D. Cranswick

91. Single Crystal Suites (also applicable to powder diffraction)
Again, a large range of programs to choose from:
Crystals for Windows - David Watkin, Richard Cooper, et al
DS*SYSTEM - Kenji Okada
ORTEX - Patrick McArdle
Platon / System S for UNIX - Ton Spek
WinGX for Windows - Louis Farrugia
Xtal (GPL’d) - Syd Hall, Doug du Boulay & R. Olthof-Hazekamp
NRCVAX - Eric Gabe, Peter White, et al
Slide 91
Lachlan M. D. Cranswick

92. WinGX for Windows single crystal suite Louis Farrugia: http://www.chem.gla.ac.uk/~louis/software/
Complete Single Crystal Suite for Windows
Links to dozens of other programs (new and old) via GUI interfaces
Nearly all programs are included with WinGX distribution
Slide 92
Lachlan M. D. Cranswick

93. WinGX for Windows single crystal suite Structure Solution
Shelxs97, Shels86, (Shelxd)
Sir97, Sir 92
Dirdif (Patterson and fragment)
Patsee fragment searching
SXGRAPH GUI with WinGX
SXGRAPH Shelxl GUI allows an easy interface for loading of fragments for passing to Patsee or Dirdif
Slide 93
Lachlan M. D. Cranswick

94. WinGX for Windows single crystal suite Refinement - Shelxl 97 (WinGX now links to Crystals as well)
GUI control of Shelx via WinGX’s SXGRAPH program
or Shelx ASCII INS File
Slide 94
Lachlan M. D. Cranswick

95. WinGX for Windows single crystal suite Hydrogen Addition options
Shelx97 (G. Sheldrick)
Manually edit INS file
Via SXGRAPH GUI
GUI XHYDEX (G Orphen)
GUI CalcOH (M Nardelli)
Slide 95
Lachlan M. D. Cranswick

96. WinGX for Windows single crystal suite Easy Interlinking with Ton Spek’s Platon
ADDSYM
Other Platon Features
Slide 96
Lachlan M. D. Cranswick

97. WinGX for Windows single crystal suite Structure Plotting
GUI WinORTEP
GUI WinSTRUPLO
Platon/Pluton/ADP
GRETEP (plugin)
Schakal (plugin)
Rasmol
Photo realistic rendering
Povray
Render / RASTER 3D
Slide 97
Lachlan M. D. Cranswick

98. Some Specialist Applications
Anharmonic Refinement
List of Software:
Incommensurate Structure Refinement
PDF / High Q Analysis
Slide 98
Lachlan M. D. Cranswick

99. Quantitative Phase Analysis
Following using Koalariet / XFIT
(fundamental parameters)
Non-trivial and in many cases, custom solutions may be required. (accurate Quantitative analysis is a complete world in itself)
Rietveld programs are commonly used for Quantitative Analysis (refer list in a previous slide).
Refer to non-Rietveld references cited in:
Slide 99
Lachlan M. D. Cranswick

100. MAUD for Java : GPL’d (you get the source code)
Tutorial on “Performing an x-ray quantitative analysis in seven easy steps!”:
Including options for standardless quantitative analysis on amorphous material
Slide 100
Lachlan M. D. Cranswick

101. Quantitative Phase Analysis - is it routinely easy?
Based on the IUCr CPD Quant Round Robin (
The answer seems to be No!
A quote from Armel Le Bail’s Tmacle “twinned refinement” software manual seems appropriate:
GOOD LUCK
IT'S VERY HARD! DON'T YOU THINK SO?
ONLY THE BOSS SAID THAT IT IS EASY,
BUT HE NEVER TRIED!
Slide 101
Lachlan M. D. Cranswick

102. Graphically interacting with the structure
Number of programs available with list available at:
Most single crystal suites include structure viewing by default but not powder refinement programs
Some can read common file formats (CIF, Shelx, etc)
Gui WinORTEP reads the widest variety of formats
Software includes: Crystals, Cameron, PIG (part of the Xtal suite), ORTEX, Gretep, Platon, GUI WinORTEP, GUI WinSTRUPLO
Gretep by Jean Laugier and Bernard Bochu
Slide 102
Lachlan M. D. Cranswick

103. Graphically interacting with the structure (more examples)
GUI WinORTEP (
GUI WinSTRUPLO (
Slide 103
Lachlan M. D. Cranswick

104. Platon: Validation - why take an interest?
For perhaps the same reason that Columbia University Law/Journalism professors teach their students (at least one - circa late 1940’s): “If your mother says she loves you,” “CHECK IT OUT!!”
If you want to solve, refine and publish structures that can stand the test of time - that means doing a variety of validation and using a variety of programs to assist in validation!
Slide 104
Lachlan M. D. Cranswick

105. Structure validation and quality checking
(Each suite can offer different features)
e.g., ORTEX by Patrick McArdle:
Example of the Void Finding and graphical viewing within ORTEX (including estimate of time to completion)
Platon can do this as well, including display of the void areas as shown on the right
Slide 105
Lachlan M. D. Cranswick

106. WinGX for Windows single crystal suite Validation and Structure Checking
Platon (Addsym, etc)
CIF Validation
Parst
GEOM
THMA 14c
IDEAL
SYMMOL
WTANAL
R-tensor
Slide 106
Lachlan M. D. Cranswick

107. Platon’s Addsym (by Ton Spek): checking for extra symmetry : e. g
Platon’s Addsym (by Ton Spek): checking for extra symmetry : e.g., Structure Published in P1 - Triclinic: 42 non-H atoms
Slide 107
Lachlan M. D. Cranswick

108. Platon’s Addsym: Correction Published in 1999: C2 - Monoclinic: 22 non-H atoms
Slide 108
Lachlan M. D. Cranswick

109. 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)
Slide 109
Lachlan M. D. Cranswick

110. Platon’s Addsym: for powders
Some powder based structures at the Royal Institution and Birkbeck College in London solved using EXPO
Triclinic P 1 - found by Addsym to be P -1
Orthorhombic:
P found by Addsym to be P n m a
P found by Addsym to be P m m n
Slide 110
Lachlan M. D. Cranswick

111. Powder diffraction pattern calculation Powder Cell for Windows
Most Rietveld Programs can calculate powder patterns but they may not be all that friendly to use
Two dedicated programs for calculating powder patterns - 1st being:
Powder Cell by Werner Kraus and Gert Nolze at BAM in Germany
Slide 111
Lachlan M. D. Cranswick

112. Powder diffraction pattern calculation Poudrix for Windows
Powder Cell by Jean Laugier and Bernard Bochu
Poudrix can handle anomalous dispersion at non X-ray tube wavelengths with the option of two models:
Brenann and Cowan
Sasaki
Slide 112
Lachlan M. D. Cranswick

113. Photorealistic hardcopy output of structures
Many programs can do this. E.g,
ORTEX (Images and Movie Animations):
Just open up a Shelx format *.INS/*.RES file and go for it
Slide 113
Lachlan M. D. Cranswick

114. Photorealistic hardcopy output of structures GUI WinORTEP / GUI Struplo / WinGX
Can open a wide variety of file formats including Shelx, CIF, GSAS, Fullprof, CDS, etc
Slide 114
Lachlan M. D. Cranswick

115. Photorealistic hardcopy output of structures Using GRETEP by Jean Laugier and Bernard Bochu
Slide 115
Lachlan M. D. Cranswick

116. Freeware for photorealistic hardcopy output of structures Balls and Sticks by Sung J. Kang & Tadashi C. Ozawa
Individual point and click creation of polyhedra and bonds via a Windows graphical user interface
Slide 116
Lachlan M. D. Cranswick

117. Photorealistic hardcopy output of Fourier Maps Marching Cubes by Michal Husak (
Interlinks with WinGX, Crystals and can read Project XD files. Software for converting GSAS Fourier files is available.
Slide 117
Lachlan M. D. Cranswick

118. Dual Boot UNIX / Windows PC and Crystallographic Nexus CD-ROMs for those isolated from the internet
Tutorials for creating dual boot Windows / UNIX PCs:
Linux
refer:
FreeBSD (can run linux binaries)
refer:
(be careful of hackers invading your systems when running Linux/UNIX. CCP14 tutorials try to be security conscious and leave no “open” services)
Free Xtal Nexus CD-ROMs for academics and students
(Supported & Sponsored by the IUCr and CCP14)
Contact the author (Lachlan Cranswick) for a free air-mailed CD-ROM.
Slide 118
Lachlan M. D. Cranswick

119. Don’t be a “passive kitten”
Just looking over someone’s shoulder will not teach you how to use this software. You have to use it yourself on your real scientific problems.
Image from:
Slide 119
Lachlan M. D. Cranswick

120. Summary http://www.ccp14.ac.uk E-mail: ccp14@dl.ac.uk
Large Genetic Diversity of Software
This diversity is necessary to help you get the job done.
Getting better all the time (some areas faster than others)
Free available for Academics and Students
Downloadable via the EPSRC funded CCP14 website:
Slide 120
Lachlan M. D. Cranswick