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
Notes Free Zone - they are on the web
http://www.ccp14.ac.uk/poster-talks/agu_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 2
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Talk Aims
• Give an overview of available
software relevant to people doing
crystallography on minerals and
inorganics
• And minor ranting about other
issues
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), submitted
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 Le Bail fitting / Rietveld
Slide 5
Using Traditional UNIT CELL refinement Methods
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Le Bail fitting: results of the volume of
Oxygen and the earth’s other core
• ~10 cc/mol (This EDX / Le Bail
result) means there can be Oxygen in
the Earth’s outer core.
• Other non diffraction results of ~15
cc/mol means there cannot be Oxygen
(shockwave / molecular dynamics)
•
Refer: “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), submitted for publication.
Slide 6
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 7
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 8
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 9
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (1 of 8)
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 10
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (2 of 8)
Cambridge Database (organics - organometallics)
• “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 11
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (3 of 8)
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 12
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 8)
Powder Methods for solving structures
• A nightmare to some
• An adventure to others!
Slide 13
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (5 of 8)
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 14
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (6 of 8)
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 15
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (7 of 8)
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)
Slide 16
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (8 of 8)
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 17
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 18
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 19
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) due
to this being the only available peer reviewed publication on this type of data
collection
Fixed Count Time
Slide 20
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 convert Madsen and Hill VCT format into GSAS ESD format
• http://www.ceramics.irl.cri.nz/Convert.htm
Slide 21
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 22
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 23
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 24
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 25
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 26
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 (normalised as FCT)
Slide 27
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 (normalised 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 (4 of 4)
Variable Count Time data (displayed as VCT)
Slide 29
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 30
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 31
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 32
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 33
•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
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 34
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 35
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 36
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 37
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 38
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Fundamental Parameters Peak Profiling mode :
fit to a low angle peak : Bragg-Brentano diffractometer data
•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
Slide 39
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 40
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 41
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 42
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 43
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 44
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 45
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 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 46
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 47
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Chekcell: Density / Z / Molecular Volume Explorer
•Easily look at effects of Z, Density and molecular volume
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
Why doesn’t this powder sample index?
Why Isn’t this cell solving
(Organometallic)
From Armel Le Bail’s site:
ESRF Synchrotron Powder Data
Very difficult problems can
still be difficult on any
available software program.
But it may solve in the
future when tried on
updated software.
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
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 52
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 53
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 54
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 55
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 - Le Bail method
can do this as peaks
positions are
constrained by the
cell and spacegroup
Slide 56
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 57
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)
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 58
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal Absorption Correction Options
• Using WinGX Single crystal suite by
Louis Farrugia as an example:
– http://www.chem.gla.ac.uk/~louis/software/wingx/
•
•
•
•
Viewing or HKL Profiles
Blessing DREAR Software
Sortav (Kappa CCD data processing)
Numerical:
CAD4 Reflection profile within
WinGX
– Gaussian, Analytical, Spherica l, Cylindrical
•
Semi Empirical:
– Psi-scans, Camel-Jockey, Multiscan
•
RefDelF:
– Difabs, XABS2, Shelxa
Slide 59
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Platon options for absorption correction
• Platon by Ton Spek:
– http://www.cryst.chem.uu.nl/platon/
•
•
•
•
•
•
•
DELrefABS
ABSPsiScan
ABSTompa
ABSGauss
ABSXtal
ABSSphere
MULscanABS
XTALHabit within Platon
• Links to FaceLift - program
to refine the initial crystal
description (HABITUS style
approach)
Slide 60
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal Indexing / Twinning
• Twinning: http://www.ccp14.ac.uk/solution/twinning/
– DIRAX for difficult Indexing problems:
• ftp://xraysoft.chem.uu.nl/pub/msdos/DIRAX/
– Twindex: ftp://laue.chem.ncsu.edu/pub/X-ray/twindex/
– The Merohedral Crystal Twinning Server:
• http://www.doe-mbi.ucla.edu/Services/Twinning/
– TWIN3.0 for Windows (test for merohedry):
• Contact V. Kahlenberg (vkahlen@uni-bremen.de)
Spacegroup Assignment:
– ABSEN Single Crystal Program by Patrick McArdle (comes with the ORTEX and
WinGX suites)
• http://www.nuigalway.ie/cryst/software.htm
• http://www.chem.gla.ac.uk/~louis/software/wingx/
– Platon spacegroup assignment options
• http://www.cryst.chem.uu.nl/platon/
Slide 61
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
ROTAX Single Crystal Twinning Software
• New ROTAX style: (Determine Twin Matrix from Fo/Fc Data)
– Platon incorporates LePageTwin
• http://www.cryst.chem.uu.nl/platon/
– WinGX and Crystals suites link seamlessly into ROTAX
(by Simon Parsons and Bob Gould)
• http://www.ccp14.ac.uk/ccp/web-mirrors/rotax/
• http://www.xtl.ox.ac.uk/
• http://www.chem.gla.ac.uk/~louis/software/
Slide 62
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 63
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 64
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 - inorganic
Slide 65
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 66
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
(not the full range of data as high angle data can be just noise and spoil the direct methods)
Slide 67
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 68
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 you in a world of not getting anywhere fast)
Slide 69
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
Thus very good for minral/inorganic structures
http://objcryst.sourceforge.net/
Slide 70
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 71
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 72
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 73
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 74
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 75
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 76
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal Structure Solution
(What’s it like to use the software?)
1) Push the “start” button
2) Structure solves
3) If not, try next program (using the benefits
of having access to multiple programs with
different strengths) Single Crystal Suites make
it trivial to easily use multiple programs
(if nothing solves, it could be twinning - or other problems?)
Slide 77
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Shelxs direct methods
(Cesium Titanium Silicate) via WinGX as an interface
Slide 78
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Sir97 direct methods with auto-building
(Cesium Titanium Silicate) via WinGX as an interface
(in this case - first try does not solve - just leave Sir97 to automatically continue on)
Slide 79
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Dirdif automatic Patterson methods
(Cesium Titanium Silicate) via WinGX as an interface
(solves and auto-builds in default mode - all atoms correctly found and labelled)
Slide 80
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 chemical crystallography dominated programs to
choose from at:
– http://www.ccp14.ac.uk/solution/xtalrefine/
•CAOS (also inside Sir97)
•Crystals
•DS*SYSTEM/LSBF
•GSAS (single crystal and powder)
•Jana (single crystal and powder)
•NRCVAX
•Shelxl
– (Shelxl is within 3 freely available crystallographic suites)
– WinGX : Platon/System S : ORTEX
•Xtal (GPL’d)
Slide 81
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal Structure Refinement Software
JANA Single Crystal and Powder Diffraction Refinement
– Developed for handling inorganics / metals - commensurate and incommensurate
– by Vaclav Petricek and Michal Dusek
– http://www-xray.fzu.cz/jana/jana.html
– Single crystal and powder diffraction (not Neutron Time of Flight (TOF))
– Powder tutorial at: http://www-xray.fzu.cz/jana/Jana2000/powders.html
– UNIX, Windows and Mac Os X
– Menu driven
– Complicated inorganic solid state structure refinement
– Commensurate, incommensurate and composite structures
– Electron density and anharmonic refinement (automatically sets the required symmetry
constraints for anharmonic)
– Refinement of f’ and f’’
– Equation editor based constraints make it possible to link any one parameter to another
– Can handle multiple twins
– Many other features
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, Jana, 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
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 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
Brian Toby’s EXPGUI Interface for GSAS
Can be 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 87
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 88
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 89
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 90
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 91
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
WinGX for Windows single crystal suite
Families of programs included/linkable with WinGX
• Importing/viewing data and
models
• Absorption Correction
• Solution (Shelx, difdif, sir, patsee)
• GUI / manual shelxl97 refinement
• Hydrogen addition options
– Shelxl, GUI CalcOH, GUI XHYDEX
• Fourier Contour Map viewing
–
Platon, Contour, Mapview, Marching cubes
• Structure Plotting
• Validation / publishing
Slide 92
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
WinGX for Windows single crystal suite
Viewing the raw CCD frames and raw profile data
•
•
•
•
Nonius Raw Frame image
files
CAD4 peak Profiles
HKLs displayed as precession
data
Simple to advanced HKL
processing, sorting, merging,
etc
Slide 93
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 94
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
WinGX for Windows single crystal suite
Absorption Correction
• Sortav for Nonius CCD data
• DREAR - Blessing software
• Numerical
– Gaussian, Analytical, Spherical,
Cylindrical, Needle
• Semi-empirical
– Psi Scans, Camel Jockey,
Multiscan
• DIFABS Style
– Difabs, Xabs, Shelxa
• Interactive Visualisation of
crystal faces using XtalView
Slide 95
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
– In the following SXGRAPH screen - only allowing heavy atom co-ords to refine
• or Shelx ASCII INS File
Slide 96
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
WinGX for Windows single crystal suite
Fourier Electron Density Contour Maps
• Use LIST 3 command in Shelxl
• Point and click map generation
• View resulting maps in:
– Contour
– Mapview
– Marching Cubes by Michak Husak
Slide 97
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 98
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 99
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 100
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)
– 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 101
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 102
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Some Specialist Applications
•
Charge Density (single crystal)
– Project XD
– http://www.chem.gla.ac.uk/~paul/paul.html
•
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 103
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Platon: Validation - why taking 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) (finding missing
symmetry): 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 - finding extra symmetry in inorganics and
minerals - P1 triclinic starting structure.
• Unpublished Mineral Example – “tiny crystal” and “marginal data”
– Default Addsym gives C2/C
• Tighten the addsym values:
– calc ADDSYM SHELX 1 0.2 0.4 0.2
– addsym gives P 2/c and exact fit on Pc
• New triclinic refinement:
• Lower R factor in Shelx
• Addsym now finds P21/c in default mode
– Thus need to be careful!
Slide 110
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 111
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 112
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 113
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 114
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 115
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Photorealistic hardcopy output of structures
Balls and Sticks - Polyhedral, etc
• http://www.toycrate.org/
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.
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
Summary
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Large Genetic Diversity of Software is out there
This diversity is necessary to help you get the job done.
Getting better all the time (some areas faster than others)
Most of it is freely available for Academics and Students
• Downloadable via the EPSRC funded CCP14 website:
http://www.ccp14.ac.uk
E-mail: ccp14@dl.ac.uk
Slide 119
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk