Crunching problems into solutions:
freely available crystallographic
software for single crystal and
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
Aims of the EPSRC funded CCP14 Project
Get free
Crystallographic
software and related
resources to
academics and
students relevant to
their research.
– Tutorials
– Software mirrors
– Mirror free
compilers and
software tools
Via: http://www.ccp14.ac.uk
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.
• Where time permits, give screen dumps
of actual examples
Slide 3
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/thai_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 4
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)
Slide 5
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 6
Using Traditional UNIT CELL refinement Methods
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
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 8
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? (2 of 4
Path of Most
Resistance?
Using a variety of “state-ofthe-art” tools can improve
versatility by allowing
different pathways and
approaches to tackle
crystallographic problems.
– When to use a scalpal
– When to unlock the
sledgehammer cabinet
– When to declare that
Defcon 1 has been
activated!
Slide 9
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Why bother knowing about freely
available software? (4 of 4)
Crystallographic
Weaponry 102
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 10
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 11
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 12
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal vs Powder diffraction (3 of 6)
Powder Methods for
solving structures
• 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 (4 of 6)
Number of structures
solved by powder
methods
• 484 up to mid 2001
• “During 2000: 58 publications”
•
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 (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 15
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)
Slide 16
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 (single crystal and powder diffraction)
Structure refinement (single crystal and powder diffraction)
Single crystal suites
Structure validation
Photorealistic rendering of crystal structures
Slide 17
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
•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 18
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 19
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Phase Identification/Search Match for Powder Diffraction 3 of 3
Multiphase mixture: Flourite, Corundum, Zincite
SampleIdent CPD RR S
Intensity (Counts) X 100000
35- 816 F LUO RI T E, SYN
46- 1212 CO RUNDUM, SYN
36- 1451 Z I NCI T E, SYN
30.00
File Name:
40.00
50.00
60.00
70.00
2-Theta Angle (deg)
c:\...\cpd-1g.cpi
Slide 20
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 21
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 22
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
A hopeful trend: 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 23
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 24
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 25
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 26
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 27
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 28
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 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)
Variable Count Time data (displayed as FCT)
(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)
Fixed Count Time data (zoomed)
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)
Variable Count Time data (displayed as FCT)
Slide 32
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 33
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 3)
Fixed Count Time
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 (2 of 3)
Variable 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 (3 of 3)
Overlaying VCT and FCT
Slide 36
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.
Slide 37
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 38
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 39
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 40
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 41
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 42
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 43
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 44
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 45
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 46
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 47
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 48
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
as well
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 49
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 50
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 51
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
•Graphics can really help sort
out errors or misassigned
Slide 52
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 53
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 54
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 55
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 56
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 57
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:
Reflection profile within WinGX
– Gaussian, Analytical, Spherica l, Cylindrical
•
Semi Empirical:
– Psi-scans, Camel-Jockey, Multiscan
•
RefDelF:
– Difabs, XABS2, Shelxa
Slide 58
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Single Crystal Absorption Correction : WinGX
Before making use of the data
(e.g., for refinement) the user is
prompted which form of
absorption corrected data to use.
Thus users can easily check the
various absorption algorithms.
Slide 59
Define and view single crystal
faces within WinGX
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:
– 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
• Summary of available software at:
– http://www.ccp14.ac.uk/solution/twinning/
• 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 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 63
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
“Specialised and Commercial” Structure Solution Programs
• 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
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
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
Single Crystal Structure Solution
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 69
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 70
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Shelxs direct methods
(tetracycline hydrochloride) via WinGX as an interface
Slide 71
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Sir direct methods and auto Fourier building
(tetracycline hydrochloride) via WinGX as an interface
Slide 72
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Dirdif Patterson methods and auto Fourier building
(tetracycline hydrochloride) via WinGX as an interface
Slide 73
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Crunch for UNIX direct methods and Fourier building
(tetracycline hydrochloride) via Platon/System S as an interface
Slide 74
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 75
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
Slide 76
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 77
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 Guided
refinement
Slide 78
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Guided structure refinement using Crystals
Import Shelx INS file of structure solved by DIRDIF
• Asymmetric unit is
always in view
Slide 79
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Guided structure refinement using Crystals
• Crystals Superviser can then
try and take the user
(including students and
chemistrs) through the
refinement - giving guidance
where appropriate
Slide 80
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Guided structure refinement using Crystals
Have now refined atom positions Isotropically
• The Crystals Supervisor
will then make further
recommendations
• (Crystals Scripts means
custom tutorials and
refinement logic can be
added)
Slide 81
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Guided structure refinement using Crystals
Have now refined atom positions anisotropically
• Atoms can be displayed
anisotropically
Slide 82
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Guided structure refinement using Crystals
Automatic Hydrogen Addition
• Graphically compare
calculated hydrogens
(white) to possible
hydrogens found in the
difference map (pink).
Slide 83
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 (who may be
learning single crystal methods
as a tool for a larger project) and displayed in organic
chemistry text books.
• May be easier teaching
crystallographic methods to a
specialist audience starting out
with their jargon.
Slide 84
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 85
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Interrupt the Guided Refinement in Crystals
Generating Fourier maps and Marching Cubes for Windows
• Easily generate Fourier
contour maps to show the
electron density. In this
case: electron density due
to the missing hydrogens.
Slide 86
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Structure refinement using Crystals
Validation via Cambridge database: geometry checking
• To students and new users, every
structure must seem like a new structure
type. Thus using CSD geometry check
can encourage students to look for errors
or novel features of the structure.
Bondlengths
RED="too long" and BLUE="too short".
RED ---- GREY ---- GREY ---- BLUE
3sigma 2sigma 1sigma 0sigma 1sigma 2sigma 3sigma
Slide 87
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Validation using Crystals
Cambridge database geometry check (1 of 4)
• Doing a CSD check
shows a bond in red
(too long) displaying
a geometry of which
is completely novel
in reference to what
is already known
Slide 88
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Validation using Crystals
Cambridge database geometry check (2 of 4)
• Using the GUI (or
scripts) make the
offending Nitrogen a
Carbon and re-refine.
Slide 89
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Validation using Crystals
Cambridge database geometry check (3 of 4)
• Black bonds around
the renamed atom
tells the user that the
new geometry has
not been tested
against the CSD. So
interrogate the CSD
again to obtain this
information.
Slide 90
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Validation using Crystals
Cambridge database geometry check (4 of 4)
• CSD results now
imply/infer that local
geometry is consistent
with what is already in
the database.
Slide 91
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 92
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 93
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 94
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 95
• 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 96
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 97
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 98
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 99
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 100
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 101
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 102
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 103
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
WinGX for Windows single crystal suite
Absorption Correction
• 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 104
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 105
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
• GUI control of Shelx via WinGX’s SXGRAPH program
• or Shelx ASCII INS File
Slide 106
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 107
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
• Squeeze/disordered solvent effects
• ADDSYM
• Other Platon Features
Slide 108
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 109
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 110
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 111
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 112
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 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 113
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/
Slide 114
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” 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!
TO HAVE THE SOLUTION DEPENDS ON YOU,
NOT ON THIS PROGRAM WHICH IS JUST
ABLE TO TEST YOUR HYPOTHESIS.......
Slide 115
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 116
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 117
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!
Slide 118
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)
Slide 119
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 120
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 121
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 122
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 123
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Platon’s Addsym - (1 of 2) finding extra symmetry in
inorganics and minerals - P1 triclinic starting structure.
• Unpublished Mineral Example
– 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
• Loosening defaults:
– calc addsym shelx exact 1 .2 .4 .4
– P-31m
Slide 124
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Platon’s Addsym - (2 of 2) finding extra symmetry in
inorganics and minerals - P1 triclinic starting structure.
• Update new refinement in triclinic:
– Lower R factor in Shelx
– Addsym now finds P21/c in default mode
• Thus need to be careful!
Slide 125
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Platon’s Addsym Be wary when using Addsym with Tilt Models
• With subtle tilts - (e.g., 0.3 A shifts)
• Increasing the Addsym defaults may
give you the ideal non-tilt model
Slide 126
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 programs for
calculating powder patterns - 1st
being:
• Powder Cell by Werner Kraus and
Gert Nolze
http://www.ccp14.ac.uk/tutorial/powdcell/
Slide 127
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 128
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 129
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 130
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 131
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 132
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 133
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk