An overview of available
software for solving crystal
structures from powder
diffraction
Lachlan 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
• Give an overview of available software
relevant to structure solution from powder
diffraction data.
• On the data collection side, mention
Variable Count Time (VCT) data collection
as something to take an active interest in as
getting the best data possible helps with the
software.
• Also mention Fundamental Parameters
peak profiling for powder indexing
Slide 2
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Notes Free Zone - they are on the web
http://www.ccp14.ac.uk/poster-talks/aca_2002a/
• 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 3
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 4
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Why bother knowing about a variety of
crystallographic software
Maximize your ability to handle
present and future scientific
problems.
Be able to cross hurdles that may
be intractable or unnecessarily
problematic if not approached the
right way.
Slide 5
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (1 of 6)
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 6
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (2 of 6)
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 7
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (2a of 6)
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 8
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 (3 of 6)
Powder Methods for solving structures
• A nightmare to some
• An adventure to others!
Slide 9
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (4 of 6)
Number of structures
solved by powder
methods
• Cumulative total of
592 up to end of 2001
– 10’s of structures added per year
•
• http://sdpd.univ-lemans.fr/iniref.html
• http://sdpd.univ-lemans.fr/iniref/SDPD-activity.html
Slide 10
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (5 of 6)
Structure Determination from Powder
Diffractometry Round Robin
• 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 11
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (6 of 6)
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 lab: 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)
• When in doubt - get a single crystal!!
Slide 12
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Talk Agenda
•Some words about data collection - Variable Count Time (VCT)
•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
Single crystal suites (also relevant to powder diffraction)
Structure validation
Photorealistic rendering of crystal structures
Slide 13
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Sample Preparation and Data Collection
• Assumption for this talk is you know the most
appropriate methods for sample preparation, hardware and
data collection.
•However, given the lack of use of Variable Count Time
(VCT) data collection, this does not seem to be the case
with data collection.
Slide 14
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., Madsen and Hill method).
Fixed Count Time
Slide 15
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 Madsen and Hill method is
at:
http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/csirominerals-anon-ftp/pub/xtallography/variable-count-time/
(Original Madsen and Hill 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.
Vctconv will inter-convert Madsen and Hill VCT format into GSAS ESD format
• http://www.ceramics.irl.cri.nz/Convert.htm
Convert4 for Windows will inter-convert x,y,esd data to GSAS ESD format
•http://www.ccp14.ac.uk/ccp/web-mirrors/ndragoe/research/software/software.html
Slide 16
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
VCT for Powder Indexing (1 of 4)
Fixed Count Time data
(data collected by Jeremy Cockcroft)
Slide 17
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
VCT for Powder Indexing (2 of 4)
Variable Count Time data (normalized as FCT)
(data collected by Jeremy Cockcroft)
Slide 18
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
VCT for Powder Indexing (3 of 4)
Fixed Count Time data (zoomed)
This peak position is not going to be very precise
Slide 19
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
VCT for Powder Indexing (3 of 4)
Variable Count Time data (zoomed)
This “trace” peak position will be more precise
Slide 20
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 21
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 (normalized as FCT)
Slide 22
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 (normalized as FCT)
Slide 23
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 24
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
– Compare to the old Enraf Nonius CAD4
single crystal diffractometer options
Something to keep an eye on - or
request from vendors.
Slide 25
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.crystalimpact.com
•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
– OpenXRD by Stefan Krumm in development (GPL’d UNIX and Windows)
Slide 26
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 27
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Find out 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
Slide 28
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 (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 29
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
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 30
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Crystallography Suites that link into the 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 31
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 32
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
•CMPR for Windows and UNIX:
– http://www.ncnr.nist.gov/programs/crystallography/
•Example of PowderX for Windows
•
•
Graphical evaluation, backtground stripping,
smoothing, alpha stripping, peak find and pass to
treor indexing
Full GUI Operation
Slide 33
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Peak Profiling for Powder indexing
•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 34
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Peak Profiling: high accuracy peak positions using
Fundamental Parameters peak profiling in XFIT
•Example of Fundamental parameters (convoluting in
the geometry elements of the diffractometer) that can
provide accurate peak positions as though your
sample was being run on an “ideal” diffractometer.
•Tutorial at:
– http://www.ccp14.ac.uk/tutorial/xfit-95/fun1.htm
•Available Fundamental Parameters Peak Profiling
and Rietveld software:
•XFIT (no longer maintained)
– http://www.ccp14.ac.uk/tutorial/xfit-95/xfit.htm
•Topas (Commercial - sequel to XFIT)
– http://www.bruker.com
•BGMN (Commercial - academic demonstration
version is freely downloadable)
– http://www.bgmn.de
•EFLECH/Index freeware from BGMN website
Slide 35
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Powder Indexing FOM Results
XFIT Fundamental Parameters peak profiling compared to
empirical Peak Fitting
Slide 36
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Powder Indexing - a non trivial endeavour
• Very tricky to solve a structure if you don’t have cell and spacegroup
• 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 37
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 38
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 39
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Chekcell : easy to see non-matching or impurity peaks
Slide 40
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 41
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
do not reliably determine
– 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 42
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Chekcell: GUI Cell transformation
•Easily transform cells and test them withing Chekcell
•Knows about common transformations
•Can manually look at sub-cells and super-cells
Slide 43
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Chekcell: Density / Z/ Mol. Vol explorer
•Easily explore values of Z, density and estimated molecular volume comparing with your found trial cells.
Slide 44
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 45
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 now 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 46
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 47
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)
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 48
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
• 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 49
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.chemeng.ucla.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 50
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Important with realspace programs to input good starting information
(too much bad or too little good can put your in a world of “not getting anywhere”)
Slide 51
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal Structure Solution
Also can be applied to powder problems - is a range of programs to choose from:
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 52
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 - and real space methods for
solving structures
•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 CORINA “energy minisation” may
generate an inaccurate 3D model where different
conformations are possible)
Slide 53
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Getting fragments into Dirdif and 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
•Or ready for powder real space structure solver
Slide 54
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
•NRCVAX
•Shelxl
–
–
–
–
(Shelxl is within 3 freely available crystallographic suites)
WinGX
Platon/System S
ORTEX
•Xtal (GPL’d)
Slide 55
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Using Crystals to help add hydrogens
Automatic Hydrogen Addition
http://www.xtl.ox.ac.uk
• Just select:
– Structure
– Add hydrogens
geometrically
• New Auto-bond
display gives extra
graphical feedback
Slide 56
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Crystals : Manual Hydrogen Addition - 1 of 2
• Crystals explains what is going on in a language organic
chemists and students can understand
Slide 57
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Crystals : Manual Hydrogen Addition - 2 of 2
• A “Wizard” then guides the
user to complete the hydrogen
addition
Slide 58
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 59
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
powerful 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 60
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 61
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 62
• 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 scales : 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 63
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Brian Toby’s EXPGUI Interface for GSAS
(This and a new combined installer makes it very easy to start using GSAS.)
http://www.ncnr.nist.gov/programs/crystallography/software/expgui/expgui_intro.html
Can spawn Ton Spek’s Platon for structure plotting and structure validation
Slide 64
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Rietveld: Rod Hill and Ian Madsen VCT data collection
•
•
•
•
Important to know how to
appropriate collect your
data that is optimized for
the analysis.
For Rietveld: If you do
have a choice of data
collection strategies for
XRD - consider variable
count time (VCT)
VCTCONV for DOS by
Mark Bowden will
convert VCT Hill and
Madsen data into GSAS
ESD format.
VCT Fortran Source Code
with references is
available
http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/csirominerals-anon-ftp/pub/xtallography/
Slide 65
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
routine as single
crystal but there
are some tutorials
with tricks on the
CCP14 website
http://www.ccp14.ac.uk/solution/restrained_rietveld/
Slide 66
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 67
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal Suites
(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 68
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 69
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 70
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 71
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 72
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 73
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 74
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
•
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 75
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Graphically interacting with the structure
(and the ability to open GSAS, Rietica and Fullprof files)
GUI WinORTEP
GUI WinSTRUPLO
(http://www.chem.gla.ac.uk/~louis/software/ortep3/)
(http://www.chem.gla.ac.uk/~louis/software/struplo/)
Slide 76
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Crystal Structure validation - Why Bother?
• Better to publish work that can stand the test of time
• Thus is very helpful doing a variety of validation and
using a variety of programs to assist in validation!
Slide 77
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 78
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 79
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Platon’s Addsym (by Ton Spek) (finding missing
symmetry): Structure Published in 1997
P1 - Triclinic: 42 non-H atoms
Slide 80
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 81
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 82
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Platon’s Addsym (by Ton Spek): for powders
• Some powder based structures at the Royal Institution and Birkbeck
College in London solved using EXPO
• Triclinic P 1 - found by Platon’s Addsym to be P -1
• Orthorhombic:
– P 21 21 21 - found by Platon’s Addsym to be P n m a
– P 2 21 21 - found by Platon’s Addsym to be P m m n
• Refer to Howard Harvey and Martin Attfield’s and Talk on the 29th May
– 10.02: From Structures to Materials Science
– 09:15 - 09:30 AM (10.02.03) (W0121)
– The Design, Synthesis, and Characterization of Novel Group IIIb
Bisphosphonate Materials.
Slide 83
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
• 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
http://www.ccp14.ac.uk/tutorial/powdcell/
Slide 84
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 85
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 86
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, Rietica, Fullprof, CDS, etc
Slide 87
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 88
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 89
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 90
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Summary
 Large Genetic Diversity of Software to help you solve
structures from powder diffraction
 This diversity is necessary to help you get the job done.
 Getting better all the time (some areas faster than others)
 Great majority of it is freely available for Academics and
Students
• Most is mirrored via the EPSRC funded CCP14 website:
http://www.ccp14.ac.uk
E-mail: ccp14@dl.ac.uk
Slide 91
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk