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.
E-mail: l.m.d.cranswick@dl.ac.uk
WWW: http://www.ccp14.ac.uk
Notes Free Zone - they are on the web
http://www.ccp14.ac.uk/poster-talks/korea_2002/
• 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 (l.m.d.cranswick@dl.ac.uk) 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.
Slide 3
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), in press.
Slide 4
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 5
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 6
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 7
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 8
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (1 of 9)
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 9
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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: http://www.ccdc.cam.ac.uk/about/annrep99/Report.html
http://www.ccdc.cam.ac.uk/prods/csd/stats.html
Slide 10
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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
Cumulative ICSD entries by date of publication
70000
2500
60000
30000
Year (19xx)
Slide 11
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 9)
Powder Methods for solving structures
• A nightmare to some
• An adventure to others!
Slide 12
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (5 of 9)
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 13
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (6 of 9)
Structure Determination from Powder
Diffractometry Round Robin 1
• Tetracycline Hydrochloride (June 1998)
– http://sdpd.univ-lemans.fr/SDPDRR/
– 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)
• http://sdpd.univ-lemans.fr/SDPDRR/sample2.html
Slide 14
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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
– http://srs.dl.ac.uk/xrd/9.8/
• 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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (9 of 9)
2nd SDPDRR (Indexing and solving):
http://www.cristal.org/sdpdrr2/
• Round robin started on Monday 9th
September
• Structure solution ending on Sunday 17th
November
Slide 17
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 18
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 19
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 20
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 :
– 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 (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
•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 22
•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 23
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
A hopeful trend: Crystallography Suites that link directly
into the crystal structure databases
Platon for UNIX (if CSD/Quest is also installed):
 http://www.cryst.chem.uu.nl/platon/
 CSD Cell searching at the click of a button
 Connectivity search: using the CORINA to generate a PDB file,
 http://www2.ccc.uni-erlangen.de/software/corina/free_struct.html
– Then use Platon/System S acting as a friendly interface for
Quest.
Slide 24
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 25
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
Other software such as GUI WinORTEP
can import a wide variety of file formats
and export these into Shelx format.
http://www.chem.gla.ac.uk/~louis/software/ortep3/
Slide 26
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 27
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 28
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 29
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 30
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 31
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 32
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)
Slide 33
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 34
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 35
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
Slide 36
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 37
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 38
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 39
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 40
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
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Powder Diffraction Utility Software
•Examining Data, peak finding, background
stripping, alpha-2 stripping
•Powder v 2.00: http://www.ccp14.ac.uk/tutorial/powder/
•Powder X, http://www.ccp14.ac.uk/tutorial/powderx/
•WinFIT,
– http://www.geol.uni-erlangen.de/html/software/soft.html
Powder X
(Alpha2 Strip, Background Strip, Peak Find)
•Winplotr, http://www-llb.cea.fr/winplotr/winplotr.htm
•XFIT, http://www.ccp14.ac.uk/tutorial/xfit-95/xfit.htm
•Example of PowderX for Windows
•
•
Graphical evaluation, backtground stripping,
smoothing, alpha stripping, peak find and pass to
treor indexing
Full GUI Operation
Slide 42
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, GPLSFT,
pearson.xls, SHADOW, Powder v2.00, PowderX, Winfit,
Winplotr, XFIT
Examples of XFIT for Windows
Slide 43
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 44
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 45
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 46
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 47
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 48
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 insulinzinc complex produced by grinding",
Acta Cryst. (2000). D56, 1549-1553.
Slide 50
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
– http://www.ccp14.ac.uk/tutorial/cmpr/
Slide 51
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://wwwcristal.org
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 (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 53
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
Slide 54
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 55
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 56
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 57
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 58
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 59
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/Uk/uk-software.htm
• 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: 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 60
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 61
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
EXPO direct methods in Action (1 of 4)
Edit the input / control file
Slide 62
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
EXPO direct methods in action (2 of 4)
Click on the OK button to start
Slide 63
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
EXPO direct methods in action (3 of 4)
Le Bail fitting of the powder pattern
Slide 64
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
EXPO direct methods in action (4 of 4)
Structure after being solved and auto built
Slide 65
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
Very user friendly in setting up rigid bodies
Includes automatic merging of atoms on special
position with dynamic occupancy correction
http://objcryst.sourceforge.net/
Slide 66
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 67
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 68
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 69
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 70
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 71
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal Structure Solution
Applicable to powder diffraction: http://www.ccp14.ac.uk/solution/xtalsolution/
•
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
– Direct Methods and automatic structure building
•
Solver – in NRCVAX Suite – based on Multan
– Direct Methods
Slide 72
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
2D to 3D model building software
•Applicable for Generating 3D fragments for Patsee/Dirdif
Orient – single crystal/powder
•Summary list at:
– http://www.ccp14.ac.uk/solution/2d_3d_model_builders/
•E.g., CORINA (COoRdINAtes) (Use web based direct
submission):
http://www2.ccc.uni-erlangen.de/software/corina/free_struct.html
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)cc
cc1C(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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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
– http://www.chem.gla.ac.uk/~louis/software/wingx/
•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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal Structure Refinement Software
(Applicable to powder diffraction for helping build up the structure)
•Range of programs to choose from:
– http://www.ccp14.ac.uk/solution/xtalrefine/
•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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Example of Crystals for Windows
David Watkin, Richard Cooper, et al.: http://www.xtl.ox.ac.uk/
• 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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Guided structure refinement using Crystals
• Automatic Hydrogen
Addition
Slide 77
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (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
• 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 (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 84
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 crystallographyfor
inserting and refining the crystal structure
 http://www.rietica.org
Slide 85
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 86
• 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 87
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 88
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 89
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Fourier capability in Rietveld Software
GSAS
(including VRML output)
Fullprof /
GFOUR for Windows
Summary list of Fourier friendly Rietveld software at:
http://www.ccp14.ac.uk/solution/rietveld_fourier_maps/
Slide 90
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal Suites
(also applicable to powder diffraction)
• Again, a large range of programs to choose from:
– http://www.ccp14.ac.uk/solution/xtalsuites/
•
•
•
•
•
•
•
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
WinGX for Windows single crystal suite
Easy Interlinking with Ton Spek’s Platon
• ADDSYM
• Other Platon Features
Slide 96
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (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 98
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 99
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 100
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 101
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 102
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Graphically interacting with the structure
(more examples)
GUI WinORTEP
GUI WinSTRUPLO
(http://www.chem.gla.ac.uk/~louis/software/ortep3/)
(http://www.chem.gla.ac.uk/~louis/software/struplo/)
Slide 103
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (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 107
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 108
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 109
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
• 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
Slide 110
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 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 111
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 112
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Photorealistic hardcopy output of structures
Many programs can do this. E.g,
ORTEX (Images and Movie
Animations):
• http://www.nuigalway.ie/cryst/
• Just open up a Shelx format
*.INS/*.RES file and go for it
Slide 113
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Photorealistic hardcopy output of structures
GUI WinORTEP / GUI Struplo / WinGX
http://www.ccp14.ac.uk/tutorial/wingx/
• Can open a wide variety of file
formats including Shelx, CIF,
GSAS, Fullprof, CDS, etc
Slide 114
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 115
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 116
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 117
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 118
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 119
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)
Free available for Academics and Students
• Downloadable via the EPSRC funded CCP14
website:
http://www.ccp14.ac.uk
E-mail: ccp14@dl.ac.uk
Slide 120
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk