![Page 1: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/1.jpg)
Dissolving 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: [email protected]
WWW: http://www.ccp14.ac.uk
![Page 2: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/2.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 2
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
![Page 3: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/3.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 3
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
![Page 4: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/4.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 4
Notes Free Zone - they are on the web
http://www.ccp14.ac.uk/poster-talks/qmul_2001/
• 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)
![Page 5: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/5.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 5
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)
![Page 6: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/6.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 6
Using the right crystallographic method can make the difference!Using Le Bail fitting / Rietveld Using Traditional UNIT CELL refinement Methods
![Page 7: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/7.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 7
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.
![Page 8: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/8.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 8
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.
![Page 9: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/9.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 9
Why bother knowing about a variety of modern software? (2 of 4)
Path of Most Resistance?
Using a variety of “state-of-the-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!
![Page 10: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/10.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 10
Why bother knowing about a variety of modern software? (3 of 4)
Crystallographic Weaponry 101
• You can benefit from having access to a variety of state of the art tools
![Page 11: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/11.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 11
Why bother knowing about freely available software? (4 of 4)
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)
Crystallographic Weaponry 102
![Page 12: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/12.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 12
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
![Page 13: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/13.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 13
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
![Page 14: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/14.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 14
Single Crystal vs Powder diffraction (3 of 6)
Powder Methods for solving structures
• Nightmare to some
• An adventure to others
![Page 15: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/15.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 15
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
![Page 16: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/16.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 16
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
![Page 17: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/17.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 17
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)
![Page 18: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/18.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 18
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
![Page 19: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/19.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 19
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
![Page 20: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/20.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 20
Phase Identification/Search Match for Powder Diffraction 2 of 3Identifying an organic – DL-Valine
33- 1954 DL-VALINE
File Name: c:\...\valine.cpi
Valine
2-Theta Angle (deg)10.00 20.00 30.00 40.00 50.00
1
Inte
nsity
(C
ount
s) X
100
000
![Page 21: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/21.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 21
Phase Identification/Search Match for Powder Diffraction 3 of 3Multiphase mixture: Flourite, Corundum, Zincite
35- 816 FLUORITE, SYN 46- 1212 CORUNDUM, SYN 36- 1451 ZINCITE, SYN
File Name: c:\...\cpd-1g.cpi
SampleIdent CPD RR S
2-Theta Angle (deg)30.00 40.00 50.00 60.00 70.00
Inte
nsity
(Cou
nts)
X 1
0000
0
![Page 22: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/22.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 22
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/
![Page 23: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/23.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 23
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/
![Page 24: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/24.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 24
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.
![Page 25: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/25.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 25
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/
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/
Example of ConvX for Windows by Mark BowdenMass data powder diffraction data converter
![Page 26: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/26.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 26
Structure Importing, Conversion and TransformationSummary list of available software at: http://www.ccp14.ac.uk/solution/structconv/
Be careful to check the resultsBest 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/
Example of Cryscon for Windows by Eric Dowty
![Page 27: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/27.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 27
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
•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
Powder X(Alpha2 Strip, Background Strip, Peak Find)
![Page 28: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/28.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 28
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
![Page 29: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/29.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 29
Peak Profiling: Crystallite size and strain using Fundamental Parameters peak profiling in XFIT
•Example of Fundamental parameters (convoluting in the geometry elements of the diffractometer) to profile peaks and also provide size and strain information (though be careful on how you intepret this)
•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 version is downloadable)
– http://www.bgmn.de
![Page 30: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/30.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 30
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 Rodriguez-Carvajal 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/
![Page 31: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/31.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 31
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:
![Page 32: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/32.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 32
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/
![Page 33: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/33.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 33
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.
![Page 34: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/34.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 34
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
![Page 35: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/35.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 35
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
![Page 36: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/36.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 36
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
![Page 37: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/37.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 37
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 insulin-zinc complex produced by grinding", Acta Cryst. (2000). D56, 1549-1553.
![Page 38: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/38.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 38
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.
![Page 39: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/39.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 39
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).
![Page 40: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/40.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 40
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 multi-phase mixture
•Graphics can really help sort out errors or misassigned
![Page 41: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/41.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 41
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
![Page 42: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/42.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 42
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
![Page 43: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/43.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 43
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
![Page 44: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/44.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 44
Unit Cell Refinement: Mass Le Bail fitting: multi-phase - overlapping patterns
Using Le Bail fitting Using Traditional Methods
![Page 45: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/45.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 45
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:• 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
MAUD (for Java PC/Mac/UNIX)Crystallite size and shape analysis
http://www.ing.unitn.it/~luttero/
![Page 46: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/46.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 46
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:– Gaussian, Analytical, Spherica l, Cylindrical
• Semi Empirical:– Psi-scans, Camel-Jockey, Multiscan
• RefDelF:– Difabs, XABS2, Shelxa
Reflection profile within WinGX
![Page 47: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/47.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 47
Single Crystal Absorption Correction : WinGX
Define and view single crystalfaces within WinGXBefore 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.
![Page 48: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/48.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 48
Platon options for absorption correction• Platon by Ton Spek:
– http://www.cryst.chem.uu.nl/platon/• DELrefABS
• ABSPsiScan
• ABSTompa
• ABSGauss
• ABSXtal
• ABSSphere
• MULscanABS
• Links to FaceLift - program to refine the initial crystal description (HABITUS style approach)
XTALHabit within Platon
![Page 49: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/49.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 49
Single Crystal Indexing / Twinning• Twinning:
– DIRAX for difficult Indexing problems: ftp://ftp.chem.uu.nl/pub/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 ([email protected])
• 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/
• ROTAX style or inspired twinning software (Fo / Fc) (by Simon Parsons and Bob Gould)
– Platon TwinRotMAt - http://www.cryst.chem.uu.nl/platon/
– ROTAX in Crystals - http://www.xtl.ox.ac.uk/crystals.html
![Page 50: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/50.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 50
“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) Monte Carlo and pseudo simulated annealing - normally use as last resort (new version for Windows has “real space molecule and fragment location”).
• http:// sdpd.univ-lemans.fr /sdpd/espoir/
• http://www.ccp14.ac.uk/ccp/web-mirrors/armel/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/
![Page 51: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/51.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 51
“Specialised and Commercial” Structure Solution Programs• ObjCryst++ & FOX - modular toolbox - including special features for inorganics
– http://objcryst.sourceforge.net/
• 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/
![Page 52: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/52.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 52
EXPO in Action (1 of 4)Edit the input / control file
![Page 53: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/53.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 53
EXPO in action (2 of 4)Click on the OK button to start
![Page 54: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/54.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 54
EXPO in action (3 of 4)Le Bail fitting of the powder pattern
![Page 55: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/55.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 55
EXPO in action (4 of 4)Structure after solved by direct methods
![Page 56: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/56.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 56
Single Crystal Structure Solution
•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
•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
•XFPA – Frantisek Pavelcik–Patterson Methods and automatic structure building
Range of programs to choose from:http://www.ccp14.ac.uk/solution/xtalsolution/
![Page 57: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/57.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 57
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?)
![Page 58: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/58.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 58
Shelxs direct methods(tetracycline hydrochloride) via WinGX as an interface
![Page 59: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/59.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 59
Sir direct methods and auto Fourier building(tetracycline hydrochloride) via WinGX as an interface
![Page 60: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/60.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 60
Dirdif Patterson methods and auto Fourier building(tetracycline hydrochloride) via WinGX as an interface
![Page 61: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/61.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 61
Crunch for UNIX direct methods and Fourier building(tetracycline hydrochloride) via Platon/System S as an interface
![Page 62: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/62.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 62
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)cccc1C(C)(O)C2CC34
(Word of warning: the “energy minisation” may generate an inaccurate 3D model where different conformations are possible)
![Page 63: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/63.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 63
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
![Page 64: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/64.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 64
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)
![Page 65: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/65.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 65
Example of Crystals for Windows David Watkin, Richard Cooper, et al.: http://www.xtl.ox.ac.uk/
• Will focus on Guided refinement
![Page 66: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/66.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 66
Guided structure refinement using Crystals Import Shelx INS file of structure solved by DIRDIF
• Asymmetric unit is always in view
![Page 67: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/67.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 67
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
![Page 68: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/68.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 68
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)
![Page 69: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/69.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 69
Guided structure refinement using Crystals Have now refined atom positions anisotropically
• Atoms can be displayed anisotropically
![Page 70: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/70.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 70
Guided structure refinement using Crystals Automatic Hydrogen Addition
• Graphically compare calculated hydrogens (white) to possible hydrogens found in the difference map (pink).
![Page 71: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/71.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 71
Interrupt the Guided Refinement in CrystalsManual 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.
![Page 72: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/72.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 72
Interrupt the Guided Refinement in Crystals Manual Hydrogen Addition - 2 of 2
• A “Wizard” then guides the user to complete the hydrogen addition
![Page 73: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/73.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 73
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.
![Page 74: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/74.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 74
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.
BondlengthsRED="too long" and BLUE="too short".
RED ---- GREY ---- GREY ---- BLUE
3sigma 2sigma 1sigma 0sigma 1sigma 2sigma 3sigma
![Page 75: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/75.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 75
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
![Page 76: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/76.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 76
Validation using Crystals Cambridge database geometry check (2 of 4)
• Using the GUI (or scripts) make the offending Nitrogen a Carbon and re-refine.
![Page 77: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/77.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 77
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.
![Page 78: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/78.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 78
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.
![Page 79: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/79.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 79
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
![Page 80: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/80.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 80
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.
![Page 81: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/81.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 81
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
• 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
![Page 82: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/82.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 82
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 high-resolution 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
![Page 83: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/83.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 83
GSAS: Individual Histogram Weighting
• In this example, you need to zoom up a bit.– XRD pattern is ~1500
times more intense than the corresponding neutron pattern
– Problematic for combined refinement
![Page 84: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/84.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 84
GSAS: Individual Histogram Weighting (use Sum(w*d**2) as a guide)• Set via EXPEDT
• (changing weight on Histogram 1 - XRD)– y !backup
– p !powder prep
– h !histograms
– f 1 !weighting on hist 1
– .001 !set the weighting
– x x x !exit expedt
• Run Powpref for new weighting to take effect
![Page 85: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/85.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 85
GSAS : Combined refinement on both XRD and Neutron
X-ray 7.6% R(F**2)
(~3.8% R Bragg)
Neutron 4.2% R(F**2)
(~2.1% R Bragg)
![Page 86: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/86.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 86
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)
• VCT Fortran Source Code with references is available
http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/csirominerals-anon-ftp/pub/xtallography/
![Page 87: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/87.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 87
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/
![Page 88: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/88.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 88
Fourier capability in Rietveld Software
GSAS (including VRML output)
Summary list of Fourier friendly Rietveld software at: http://www.ccp14.ac.uk/solution/rietveld_fourier_maps/
Fullprof /
GFOUR for Windows
![Page 89: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/89.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 89
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
![Page 90: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/90.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 90
WinGX for Windows single crystal suiteLouis 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
![Page 91: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/91.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 91
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
![Page 92: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/92.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 92
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
![Page 93: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/93.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 93
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
![Page 94: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/94.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 94
WinGX for Windows single crystal suite Refinement - Shelxl 97
• GUI control of Shelx via WinGX’s SXGRAPH program
• or Shelx ASCII INS File
![Page 95: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/95.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 95
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)
![Page 96: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/96.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 96
WinGX for Windows single crystal suite Easy Interlinking with Ton Spek’s Platon
• Squeeze/disordered solvent effects
• ADDSYM
• Other Platon Features
![Page 97: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/97.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 97
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
![Page 98: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/98.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 98
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
![Page 99: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/99.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 99
WinGX for Windows single crystal suite Validation and Structure Checking
• Platon (Addsym, etc)
• CIF Validation
• Parst
• GEOM
• THMA 14c
• IDEAL
• SYMMOL
• WTANAL
• R-tensor
![Page 100: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/100.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 100
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/
![Page 101: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/101.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 101
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).
• Maud for Java Quantitative Analysis Tutorial:http://www.ing.unitn.it/~luttero/maud/tutorial/
• 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/
![Page 102: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/102.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 102
Quantitative Phase Analysis - pharmaceuticals•No-one using a Rietveld method could take on the IUCr CPD QARR samples due to lack of crystal structures.
•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.......
From the IUCr CPD Quant Round Robin(draft results for publication)
http://www.iucr.org/iucr-top/comm/cpd/QARR/
![Page 103: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/103.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 103
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
Gretep by Jean Laugier and Bernard Bochuhttp://www.ccp14.ac.uk/tutorial/lmgp/#gretep
![Page 104: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/104.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 104
Graphically interacting with the structure (more examples)
GUI WinORTEP (http://www.chem.gla.ac.uk/~louis/software/ortep3/)
GUI WinSTRUPLO (http://www.chem.gla.ac.uk/~louis/software/struplo/)
![Page 105: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/105.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 105
Crystal Structure validation - Why Bother?• 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!!”
• Better to publish work that can stand the test of time - thus is very helpful doing a variety of validation and using a variety of programs to assist in validation!
![Page 106: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/106.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 106
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)
![Page 107: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/107.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 107
WinGX for Windows single crystal suite Validation and Structure Checking
• Platon (Addsym, etc)
• CIF Validation
• Parst
• GEOM
• THMA 14c
• IDEAL
• SYMMOL
• WTANAL
• R-tensor
![Page 108: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/108.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 108
Platon’s Addsym (by Ton Spek): Structure Published in 1997
P1 - Triclinic: 42 non-H atoms
![Page 109: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/109.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 109
Platon’s Addsym: Correction Published in 1999: C2 - Monoclinic: 22 non-H atoms
![Page 110: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/110.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 110
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)
![Page 111: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/111.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 111
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
![Page 112: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/112.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 112
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!
![Page 113: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/113.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 113
Powder diffraction pattern calculationPowder 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/
![Page 114: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/114.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 114
Powder diffraction pattern calculationPoudrix 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
![Page 115: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/115.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 115
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
![Page 116: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/116.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 116
Photorealistic hardcopy output of structuresGUI 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
![Page 117: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/117.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 117
Photorealistic hardcopy output of Fourier MapsMarching Cubes by Michal Husak
(http://www.ccp14.ac.uk/tutorial/marchingcube/)
• Interlinks with WinGX, Crystals and can read Project XD files.
![Page 118: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/118.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 118
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 freeair-mailed CD-ROM.
![Page 119: L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for](https://reader036.vdocuments.us/reader036/viewer/2022062408/56813c5a550346895da5d963/html5/thumbnails/119.jpg)
Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.ukSlide 119
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.ukE-mail: [email protected]