What can freely available powder
diffraction software via the Internet
do for you?
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.
E-mail: l.m.d.cranswick@dl.ac.uk
WWW: http://www.ccp14.ac.uk
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.
• Most software described can be freely
usable by anyone
Slide 2
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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), 23
November 2002
.
Slide
3
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Using the right crystallographic method can make the difference!
Using Traditional UNIT CELL refinement Methods
Slide 4
Using Le Bail fitting / Rietveld
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 5
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Why bother knowing about a variety of modern software? (1 of 2)
Path of Most
Resistance?
Using a variety of “stateof-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 6
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 7
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 8
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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:
http://www.ccp14.ac.uk/solution/powderdataconv/
Example of ConvX for Windows by Mark Bowden
Mass data powder diffraction data converter
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:
 http://www.lancs.ac.uk/people/cpaap/pfe/
Freeware ConTEXT Editor for Windows (does column
editing)
 http://www.fixedsys.com/context/
Slide 9
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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
http://www.icdd.com
– Alternative being developed is the Pauling File: http://www.pauling.com
• 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:
– http://www.ccp14.ac.uk/solution/search-match.htm
– 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 10
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Phase Identification/Search Match for Powder Diffraction 2 of 3
Identifying an organic – DL-Valine
Valine
3 3 - 1 9 5 4 D L-V A LI N E
Intensity (Counts) X 100000
1
10.00
File Name:
20.00
30.00
40.00
50.00
2-Theta Angle (deg)
c:\...\valine.cpi
Slide 11
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Which software, databases and methods work the best:
Search Match Round Robin (2nd May 2002 to 30th June 2002):
http://sdpd.univ-lemans.fr/smrr/ and CCP14 mirrors
•Conclusions :
– Accurate 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 12
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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):
– http://cds3.dl.ac.uk/cds/cds.html
– Dutch equivalent is the CMBI at: http://www.cmbi.kun.nl/cheminf/
•ICSD (Minerals and Inorganics)
– http://www.fiz-karlsruhe.de/
– Web accessible demonstration:
– http://barns.ill.fr/dif/icsd/
•MDF/CRYSTMET
– (Metals and Alloys)
– http://www.tothcanada.com
•CCSD
– (Organics and Organometallics)
– http://www.ccdc.cam.ac.uk/
Slide 13
•American Mineralogist
– http://www.geo.arizona.edu/xtal-cgi/test/
•WWW Mincryst
– http://database.iem.ac.ru/mincryst/
– 2398 unique phases - most with
crystal structure data
•Mineral web
– http://www.minweb.co.uk
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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.
– http://barns.ill.fr/dif/icsd/
Slide 14
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
New for 2003: C.O.D.
http://www.crystallography.net/
Crystallography Open
Database - scientists deposit
their own archive of CIF
structure files which are
generally accessible.
(includes all the American
Mineralogist structures)
Slide 15
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Structure Importing, Conversion and Transformation
Summary list of available software at:
http://www.ccp14.ac.uk/solution/structconv/
Example of Cryscon for Windows by Eric Dowty
Be careful to check the results
Best program for the moment is the
shareware Cryscon
 http://www.shapesoftware.com
Slide 16
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 17
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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
Slide 18
Variable Count Time
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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, 385392 http://www.iucr.org/cgi-bin/paper?hz0014
Philips Friendly Fortran source code that does this Hill and Madsen method is
at:
http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/csirominerals-anon-ftp/pub/xtallography/variable-count-time/
(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 19
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
VCT for trace Phase ID (1 of x)
Fixed Count Time data
(data collected by Jeremy Cockcroft)
Slide 20
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
VCT for trace Phase ID (1 of x)
Variable Count Time data (displayed as FCT)
(data collected by Jeremy Cockcroft)
Slide 21
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
VCT for trace Phase ID (1 of x)
Fixed Count Time data (zoomed)
Slide 22
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
VCT for trace Phase ID (1 of x)
Variable Count Time data (displayed as FCT)
(you only need to count excessively in the relevant angular ranges)
Slide 23
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 24
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
VCT to aid in phase ID and profile fitting (1 of 2)
Fixed Count Time
Slide 25
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
VCT to aid in phase ID and profile fitting (2 of 2)
Variable Count Time
(you only need to count excessively in the relevant angular ranges)
Slide 26
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
VCT for Structure Solution and Refinement (1 of 4)
Variable Count Time data (as collected)
Slide 27
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
VCT for Structure Solution and Refinement (2 of 4)
Variable Count Time data (displayed as FCT)
Slide 28
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
VCT for Structure Solution and Refinement (3 of 4)
Variable Count Time data (displayed as FCT)
Slide 29
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
VCT for Structure Solution and Refinement (4 of 4)
Variable Count Time data (displayed as VCT)
Slide 30
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Where is VCT Data Collection?
Not a routine or available option in
majority of commercial XRD
control software
Something to keep an eye on - or
request from vendors.
VCT is in the new Bede powder diffraction system
Slide 31
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Peak Profiling
(indexing, unit cell refinement, size/strain, etc)
For Overall Summary of available peak
profiling software refer to:
http://www.ccp14.ac.uk/solution/peakprofiling/
These include: CMPR, DRXWin, EFLECH, Fityk
(GPL’d);GPLSFT, pearson.xls, SHADOW, Powder
v2.00, PowderX, Winfit, Winplotr, XFIT
Examples of XFIT for Windows
(includes fundamental parameters
peak profiling)
Slide 32
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Powder Indexing - a non trivial endeavour
• For Overall Summary of available powder indexing software refer
to:
http://www.ccp14.ac.uk/solution/indexing/
• 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 RodriguezCarvajal for indexing Super Cell and Incommensurate cells.
(available within Winplotr)
http://www-llb.cea.fr/winplotr/winplotr.htm
ftp://bali.saclay.cea.fr/pub/divers/fullprof.2k/
Slide 33
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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.
http://www.ccp14.ac.uk/tutorial/crys/
Example of
CRYSFIRE Screen
prompting the saving
into one of 8 different
indexing program
formats:
Slide 34
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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.
http://www.ccp14.ac.uk/tutorial/lmgp/
Slide 35
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 36
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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. 42-60 (1957)”
•Efficient Sub-cell and
super-cell searching,
then easy reviewing of
newly derived cells
within the Chekcell
interface
Slide 37
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Some Alternatives to Crysfire: Winplotr, PowderX
Winplotr by Juan Rodriguez-Carvajal
– http://www-llb.cea.fr/fullweb/powder.htm
PowderX by Cheng Dong
– http://www.ccp14.ac.uk/tutorial/powderx/
Powder v2 by Nita Dragoe
– http://www.ccp14.ac.uk/tutorial/powder/
CMPR for Windows and UNIX by Brian
Toby (with source code)
– http://www.ccp14.ac.uk/tutorial/cmpr/
Slide 38
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
New MCMaille by Armel Le Bail (Sep 2002)
by Armel Le Bail
– http://www.cristal.org
Monte Carlo Cell finding / indexing
software
Whole Profile method using reconstituted
peaks positions and intensities
Not sensitive to trace impurities
Latest version can works almost as fast as
Dicvol
Poor data can still give no reasonable
result.
Slide 39
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Updated MCMaille - December 2002
Can “try” and index 2 phase materials
Very experimental “2 phase”
desparation option
Could be far better to go back
into the lab and try and
separate out the phases
As it is distributed with the
source code - you can make
your own modifications and
add features.
Slide 40
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Unit Cell Refinement (powders)
•For Overall Summary of available unit cell refinement software
refer to:
http://www.ccp14.ac.uk/solution/unitcellrefine/
•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 41
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
CELREF for Unit Cell Refinement
•by Jean Laugier and
Bernard Bochu
http://www.ccp14.ac.uk/tutorial/lmgp/
•In this example, celref is
performing graphical Unit Cell
refinement on calcite in a multiphase mixture
Knows about spacegroups
Graphics can really help sort
out errors or misassigned hkls
Slide 42
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Full Profile Fitting (Powder)
•For Overall Summary of available full profile analysis refer to:
Le Bail based: http://www.ccp14.ac.uk/solution/lebail/
Pawley Based: http://www.ccp14.ac.uk/solution/pawley/
•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 43
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Le Bail full profile fitting - Rietica Rietveld
•By Brett Hunter
– http://www.rietica.org
– http://www.ccp14.ac.uk/tutorial/lhpm-rietica/
•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 44
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 45
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Unit Cell Refinement: Mass Le Bail fitting: multi-phase - overlapping patterns
Using Le Bail fitting
Slide 46
Using Traditional Methods
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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:
•
MAUD (for Java PC/Mac/UNIX)
Crystallite size and shape analysis
http://www.ing.unitn.it/~luttero/
http://www.ccp14.ac.uk/solution/pole_figure/
–
–
–
–
–
–
–
BEARTEX for Windows
GSAS Rietveld (Windows/UNIX)
MAUD for Java
POFINT
popLA
Symmet for DOS
TexturePlus for Windows
Slide 47
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Solving Structures:
Single Crystal vs Powder diffraction (1 of 5)
Single Crystal
• “Mass transit” structure
solution and refinement
• There are difficulties:
– Crystal not representative
of the bulk
– Twinning
– Crystal decomposes during
data collection
– “Difficult” structure
Slide 48
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (2 of 5)
Cambridge Database
• (that Scale is in the 100’s of thousands)
– 2001 report: http://www.ccdc.cam.ac.uk/about/annrep2001/report.html
– http://www.ccdc.cam.ac.uk/prods/csd/csd.html
Slide 49
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (3 of 5)
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
Cumulative ICSD entries by date of publication
70000
2500
60000
30000
Year (19xx)
Slide 50
Year (19xx)
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
97
89
81
73
65
57
49
41
97
89
81
73
65
57
49
41
33
0
25
0
17
10000
9
500
33
20000
25
1000
40000
17
1500
50000
9
2000
1
Publications
3000
1
Publications
ICSD entries by date of publication
Single Crystal vs Powder diffraction (4 of 5)
Powder Methods for solving structures
• A nightmare to some
• An adventure to others!
Slide 51
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (5 of 5)
Number of structures
solved by powder
methods
• 592 up to end of 2001
• http://sdpd.univ-lemans.fr/iniref.html
• http://sdpd.univ-lemans.fr/iniref/SDPD-activity.html
Slide 52
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Structure Solution from Powder Diffraction Round Robins
1st SDPD Round Robin - 1998:
(Solving only):
http://www.cristal.org/SDPDRR/
2nd SDPD Round Robin - 2002:
(Indexing and solving):
http://www.cristal.org/sdpdrr2/
• Indexing:
– Only 6 submissions (6% return rate)
– Only Index/EFLECH by Joerg
Bergmann was able to suggest
solutions for samples 4 to 8 within
the time limit.
• Solving:
• 70 Downloads of data
• Only two submissions using:
– CSD System from Stoe
– Druid/Mystic (now called Dash)
Slide 53
• Solving:
• >100 Downloads of data
• Only two submissions using:
– Fox (GPL’d - free)
– Topas (commercial from Bruker)
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
“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
– http://www.irmec.ba.cnr.it/
• If EXPO fails, it is possible to use Le Bail or Pawley extracted data with Single Crystal
Structure Solution Software:
– http://www.ccp14.ac.uk/solution/xtalsolution/
• 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: http://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: http://sdpd.univ-lemans.fr/sdpd/espoir/10mn/
– FOX: http://objcryst.sourceforge.net/
Slide 54
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
“Specialised and Commercial” Structure Solution Programs
• PSSP – molecular structures
– http://powder.physics.sunysb.edu/programPSSP/pssp.html
• ZEFSA II – for Zeolites (GPL’d)
– http://www.mwdeem.rice.edu/zefsaII/
• Focus – for Zeolites
– http://www.kristall.ethz.ch/LFK/software/
• 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: http://www.accelrys.com
Crystal Structure Determination Package (WinCSD/CSD) : http://imr.chem.binghamton.edu/zavalij/CSD.html
DASH (Druid and Mystic of old): http://www.ccdc.cam.ac.uk/prods/dash/
TOPAS : http://www.bruker-axs.com
Endeavour : http://www.crystalimpact.com/endeavour/
Slide 55
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
New FOX real space structure solution by
Vincent Favre-Nicolin and Radovan Cerny
Available for UNIX/Linux and MS-Windows
GUI Based
Is friendly in setting up of rigid bodies
Includes automatic merging of atoms on special
position with dynamic occupancy correction
http://objcryst.sourceforge.net/
Slide 56
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Adding polyhedra in Fox - 1 of 5
Click on “Crystals”, “Scatterers” Icon, “Add”
Slide 57
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Adding polyhedra in Fox - 2 of 5
Select the central atom
Slide 58
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Adding polyhedra in Fox - 3 of 5
Select the corner atom(s)
Slide 59
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Adding polyhedra in Fox - 4 of 5
Give the Bond length
Slide 60
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Adding polyhedra in Fox - 5 of 5
Done!
Slide 61
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Structure Refinement using Powder Diffraction Data
(Rietveld Refinement)
•
Large range of programs to choose from:
– http://www.ccp14.ac.uk/mirror/mirror.htm
– http://www.ccp14.ac.uk/solution/rietveld_software/
• 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, Quanto, Riet7/SR5, Rietan 2000 (GPL’d)
Rietquan, Simref, WinMprof, XND, XRS-82/DLS-76
Slide 62
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 63
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Rietveld Programs - Rietica by Brett Hunter
 Full Graphical User Interface
 Still got to appreciate and know your crystallography for inserting and
refining the crystal structure
 http://www.rietica.org
Slide 64
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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
Slide 65
• GSAS resources, tutorials and links
(including links to EXPGUI)
– http://www.ccp14.ac.uk/solution/gsas/
• 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
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 highresolution X-ray powder
diffraction data: a variant of
T3R3 human insulin-zinc
complex produced by
grinding", Acta Cryst. (2000).
D56, 1549-1553.
http://journals.iucr.org/d/issues/2000/12/00/issconts.html
Slide 66
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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.)
http://www.ncnr.nist.gov/programs/crystallography/software/expgui/expgui_intro.html
Slide 67
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Restrained Rietveld structure refinement of organics
• Software not as
powerful as single
crystal but there
are some tutorials
with tricks on the
CCP14 website
http://www.ccp14.ac.uk/solution/restrained_rietveld/
Slide 68
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Fourier capability in Rietveld Software
Example of GSAS
2D contour maps and also VRML output (below)
Summary list of Fourier friendly Rietveld software at:
http://www.ccp14.ac.uk/solution/rietveld_fourier_maps/
Slide 69
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Some Specialist Applications
• Anharmonic Refinement
– List of Software:
– http://www.ccp14.ac.uk/solution/anharmonic/
• Incommensurate Structure Refinement
– List of Software:
– http://www.ccp14.ac.uk/solution/incomm.htm
• PDF / High Q Analysis
– List of Software:
– http://www.ccp14.ac.uk/solution/high_q_pdf/
Slide 70
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Quantitative Phase Analysis
•
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:
Following using Koalariet / XFIT
(fundamental parameters)
http://www.ccp14.ac.uk/tutorial/xfit-95/
http://www.ccp14.ac.uk/poster-talks/david-hay-quant-notes-axaa99/
Slide 71
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
MAUD for Java : GPL’d
(you get the source code)
Tutorial on “Performing an x-ray quantitative analysis in seven easy steps!”:
http://www.ing.unitn.it/~luttero/maud/tutorial/
http://www.ccp14.ac.uk/ccp/web-mirrors/lutterotti/~luttero/maud/tutorial/
Including options for standardless quantitative analysis on
amorphous material
Slide 72
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
New for 2002: Fullpat (runs within MS-Excel)
By Steve Chipera and Dave Bish of Los Alamos National Laboratory, USA
http://www.ccp14.ac.uk/ccp/web-mirrors/fullpat/
Full profile non-Rietveld method using standards
Described in the IUCr Commission on Powder Diffraction Newsletter:
http://www.se.iucr.org/iucr-top/comm/cpd/Newsletters/no27jul2002/
Slide 73
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
New for 2003: Rockjock (runs within MS-Excel)
By Dennis D. Eberl of the USGS
ftp://brrcrftp.cr.usgs.gov/pub/ddeberl/
Full profile non-Rietveld method using standards
Described in the next IUCr Commission on Powder Diffraction Newsletter:
http://www.se.iucr.org/iucr-top/comm/cpd/Newsletters/
Slide 74
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Quantitative Phase Analysis - is it routinely easy?
Based on the IUCr CPD Quant Round Robin
(http://www.iucr.org/iucr-top/comm/cpd/QARR/)
The answer seems to be No!
A quote from Armel Le Bail’s Tmacle “twinned refinement”
software manual seems appropriate:
http://sdpd.univ-lemans.fr/museum/tmacle92.zip
GOOD LUCK
IT'S VERY HARD! DON'T YOU THINK SO?
ONLY THE BOSS SAID THAT IT IS EASY,
BUT HE NEVER TRIED!
Slide 75
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Graphically interacting with the structure
•
Number of programs available
with list available at:
http://www.ccp14.ac.uk/solution/structuredrawing/
•
Most single crystal suites include
structure viewing by default but
not powder refinement programs
•
Some can read common file
formats (CIF, Shelx, etc)
Gretep by Jean Laugier and Bernard Bochu
http://www.ccp14.ac.uk/tutorial/lmgp/#gretep
– 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
Slide 76
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 publish anything that can stand the test of time - you
need to be validating your results as much as possible.
Slide 77
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Platon’s Addsym (by Ton Spek): checking for extra
symmetry : e.g., Structure Published in 1997
P1 - Triclinic: 42 non-H atoms
Slide 78
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Platon’s Addsym: Correction Published in 1999:
C2 - Monoclinic: 22 non-H atoms
Slide 79
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 80
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Platon’s Addsym: for powders
• Some powder based structures at the Royal Institution
and Birkbeck College in London solved using
EXPO direct methods
• Triclinic P 1 - found by Addsym to be P -1
• Orthorhombic:
– P 21 21 21 - found by Addsym to be P n m a
– P 2 21 21 - found by Addsym to be P m m n
• Platon is not free for commercial use
Slide 81
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 GUI programs for
calculating powder patterns - 1st
being:
• Powder Cell by Werner Kraus and
Gert Nolze at BAM in Germany
http://www.ccp14.ac.uk/tutorial/powdcell/
Slide 82
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Powder diffraction pattern calculation
Poudrix for Windows
• Powder Cell by Jean Laugier
and Bernard Bochu
http://www.ccp14.ac.uk/tutorial/lmgp/#pdw
• Poudrix can handle anomalous
dispersion at non X-ray tube
wavelengths with the option of
two models:
– Brenann and Cowan
– Sasaki
Slide 83
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Photorealistic hardcopy output of structures
Using GRETEP by Jean Laugier and Bernard Bochu
http://www.ccp14.ac.uk/tutorial/lmgp/
http://www.ccp14.ac.uk/ccp/web-mirrors/lmgp-laugier-bochu/
Slide 84
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Freeware for photorealistic hardcopy output of structures
Balls and Sticks by Sung J. Kang & Tadashi C. Ozawa
• http://www.toycrate.org
• http://www.ccp14.ac.uk/ccp/web-mirrors/toycrate/
• Individual point and click creation of polyhedra and bonds via
a Windows graphical user interface
Slide 85
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Photorealistic hardcopy output of Fourier Maps
Marching Cubes by Michal Husak
(http://www.ccp14.ac.uk/tutorial/marchingcube/)
• Interlinks with WinGX, Crystals and
can read Project XD files. Software
for converting GSAS Fourier files is
available.
Slide 86
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Other Internet Resources
• Crystallographic Mailing lists and internet newsgroups:
– http://www.ccp14.ac.uk/maillist/
– Including:
•
•
•
•
•
Sci.techniques.xtallography Internet newsgroup
Rietveld Users’ Mailing List
SDPD - Structure Determination from Powder Diffractometery
XRD - discussions on X-ray Diffraction Hardware
Clay Minerals Mailing List
• IUCr Commission on Powder Diffraction Newsletter:
– http://www.iucr.org/iucr-top/comm/cpd/Newsletters/
Slide 87
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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: http://www.ccp14.ac.uk/solution/linux/
• FreeBSD (can run linux binaries)
– refer: http://www.ccp14.ac.uk/solution/bsdunix/
•
(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
http://www.unige.ch/crystal/stxnews/nexus/index.htm
(Supported & Sponsored by the IUCr and CCP14)
Contact the author (Lachlan Cranswick) for a free
air-mailed CD-ROM.
Slide 88
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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: http://www.cs.umbc.edu/~rheingan/SIGGRAPH/motion.slides.pdf
Slide 89
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Summary




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)
Freely available for Academics and Students
 Much is free for commercial applications
• Downloadable via the EPSRC funded CCP14
website:
http://www.ccp14.ac.uk
E-mail: ccp14@dl.ac.uk
Slide 90
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk