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. WWW:

Lachlan M. D. Cranswick Slide 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:

Lachlan M. D. Cranswick Slide 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

Lachlan M. D. Cranswick Slide 4 Notes Free Zone - they are on the web 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)

Lachlan M. D. Cranswick Slide 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)

Lachlan M. D. Cranswick Slide 6 Using the right crystallographic method can make the difference! Using Le Bail fitting / Rietveld Using Traditional UNIT CELL refinement Methods

Lachlan M. D. Cranswick Slide 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.

Lachlan M. D. Cranswick Slide 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.

Lachlan M. D. Cranswick Slide 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!

Lachlan M. D. Cranswick Slide 10 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

Lachlan M. D. Cranswick Slide 11 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

Lachlan M. D. Cranswick Slide 12 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: –

Lachlan M. D. Cranswick Slide 13 Single Crystal vs Powder diffraction (3 of 6) Powder Methods for solving structures Nightmare to some An adventure to others

Lachlan M. D. Cranswick Slide 14 Single Crystal vs Powder diffraction (4 of 6) Number of structures solved by powder methods 484 up to mid 2001 “During 2000: 58 publications”

Lachlan M. D. Cranswick Slide 15 Single Crystal vs Powder diffraction (5 of 6) Structure Determination from Powder Diffractometry Round Robin Tetracycline Hydrochloride (June 1998) – –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)

Lachlan M. D. Cranswick Slide 16 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 – 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)

Lachlan M. D. Cranswick Slide 17 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

Lachlan M. D. Cranswick Slide 18 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 –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: – –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)

Lachlan M. D. Cranswick Slide 19 Phase Identification/Search Match for Powder Diffraction 2 of 3 Identifying an organic – DL-Valine

Lachlan M. D. Cranswick Slide 20 Phase Identification/Search Match for Powder Diffraction 3 of 3 Multiphase mixture: Flourite, Corundum, Zincite

Lachlan M. D. Cranswick Slide 21 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): – ICSD (Inorganics) – –Web accessible demonstration: – MDF/CRYSTMET –(Metals and Alloys) – CCSD –(Organics and Organometallics) –

Lachlan M. D. Cranswick Slide 22 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. –

Lachlan M. D. Cranswick Slide 23 A hopeful trend: Crystallography Suites that link into the structure databases  Platon for UNIX (if CSD/Quest is also installed):   CSD Cell searching at the click of a button  Connectivity search: using the CORINA to generate a PDB file,  –Then use Platon/System S acting as a friendly interface for Quest.

Lachlan M. D. Cranswick Slide 24 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:  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:   Freeware ConTEXT Editor for Windows (does column editing)  Example of ConvX for Windows by Mark Bowden Mass data powder diffraction data converter

Lachlan M. D. Cranswick Slide 25 Structure Importing, Conversion and Transformation  Summary list of available software at:  Be careful to check the results  Best program for the moment is the shareware Cryscon   Other software such as GUI WinORTEP can import a wide variety of file formats and export these into Shelx format. Example of Cryscon for Windows by Eric Dowty

Lachlan M. D. Cranswick Slide 26 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

Lachlan M. D. Cranswick Slide 27 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 TimeVariable Count Time

Lachlan M. D. Cranswick Slide 28 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, Philips Friendly Fortran source code that does this Hill and Madsen method is at: (Original Hill and Madsen VCT (variable count time) Paper), I. C. Madsen and R. J. Hill, Adv. X-ray Anal. (1992), 35, 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.

Lachlan M. D. Cranswick Slide 29 VCT for trace Phase ID (1 of x) Fixed Count Time data (data collected by Jeremy Cockcroft)

Lachlan M. D. Cranswick Slide 30 VCT for trace Phase ID (1 of x) Variable Count Time data (displayed as FCT) (data collected by Jeremy Cockcroft)

Lachlan M. D. Cranswick Slide 31 VCT for trace Phase ID (1 of x) Fixed Count Time data (zoomed)

Lachlan M. D. Cranswick Slide 32 VCT for trace Phase ID (1 of x) Variable Count Time data (displayed as FCT)

Lachlan M. D. Cranswick Slide 33 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

Lachlan M. D. Cranswick Slide 34 VCT to aid in phase ID and profile fitting (1 of 3) Fixed Count Time

Lachlan M. D. Cranswick Slide 35 VCT to aid in phase ID and profile fitting (2 of 3) Variable Count Time

Lachlan M. D. Cranswick Slide 36 VCT to aid in phase ID and profile fitting (3 of 3) Overlaying VCT and FCT

Lachlan M. D. Cranswick Slide 37 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.

Lachlan M. D. Cranswick Slide 38 Powder Diffraction Utility Software Examining Data, peak finding, background stripping, alpha-2 stripping Powder v 2.00: Powder X, WinFIT, – Winplotr, XFIT, 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)

Lachlan M. D. Cranswick Slide 39 Peak Profiling (indexing, unit cell refinement, size/strain, etc) For Overall Summary of available peak profiling software refer to: These include: CMPR, DRXWin, EFLECH, GPLSFT, pearson.xls, SHADOW, Powder v2.00, PowderX, Winfit, Winplotr, XFIT Examples of XFIT for Windows

Lachlan M. D. Cranswick Slide 40 Powder Indexing - a non trivial endeavour For Overall Summary of available powder indexing software refer to: 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) ftp://bali.saclay.cea.fr/pub/divers/fullprof.2k/

Lachlan M. D. Cranswick Slide 41 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. Example of CRYSFIRE Screen prompting the saving into one of 8 different indexing program formats:

Lachlan M. D. Cranswick Slide 42 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.

Lachlan M. D. Cranswick Slide 43 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.

Lachlan M. D. Cranswick Slide 44 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 (1957)” Efficient Sub-cell and super-cell searching, then easy reviewing of newly derived cells within the Chekcell interface

Lachlan M. D. Cranswick Slide 45 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

Lachlan M. D. Cranswick Slide 46 Chekcell: Density / Z / Molecular Volume Explorer Easily look at effects of Z, Density and molecular volume

Lachlan M. D. Cranswick Slide 47 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

Lachlan M. D. Cranswick Slide 48 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,

Lachlan M. D. Cranswick Slide 49 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.

Lachlan M. D. Cranswick Slide 50 Some Alternatives to Crysfire: Winplotr, PowderX Winplotr by Juan Rodriguez-Carvajal – PowderX by Cheng Dong – Powder v2 by Nita Dragoe – CMPR for Windows and UNIX by Brian Toby –

Lachlan M. D. Cranswick Slide 51 Unit Cell Refinement (powders) For Overall Summary of available unit cell refinement software refer to: 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).

Lachlan M. D. Cranswick Slide 52 CELREF for Unit Cell Refinement by Jean Laugier and Bernard Bochu 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

Lachlan M. D. Cranswick Slide 53 Full Profile Fitting (Powder) For Overall Summary of available full profile analysis refer to: Le Bail based: Pawley Based: 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

Lachlan M. D. Cranswick Slide 54 Le Bail full profile fitting - Rietica Rietveld By Brett Hunter – – 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

Lachlan M. D. Cranswick Slide 55 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

Lachlan M. D. Cranswick Slide 56 Unit Cell Refinement: Mass Le Bail fitting: multi-phase - overlapping patterns Using Le Bail fittingUsing Traditional Methods

Lachlan M. D. Cranswick Slide 57 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: –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

Lachlan M. D. Cranswick Slide 58 Single Crystal Absorption Correction Options Using WinGX Single crystal suite by Louis Farrugia as an example: – 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

Lachlan M. D. Cranswick Slide 59 Single Crystal Absorption Correction : WinGX Define and view single crystal faces within 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.

Lachlan M. D. Cranswick Slide 60 Platon options for absorption correction Platon by Ton Spek: – DELrefABS ABSPsiScan ABSTompa ABSGauss ABSXtal ABSSphere MULscanABS Links to FaceLift - program to refine the initial crystal description (HABITUS style approach) XTALHabit within Platon

Lachlan M. D. Cranswick Slide 61 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: TWIN3.0 for Windows (test for merohedry): Contact V. Kahlenberg Spacegroup Assignment: ABSEN Single Crystal Program by Patrick McArdle (comes with the ORTEX and WinGX suites) – – Platon spacegroup assignment options –

Lachlan M. D. Cranswick Slide 62 ROTAX Single Crystal Twinning Software Summary of available software at: – New ROTAX style: (Determine Twin Matrix from Fo/Fc Data) –Platon incorporates LePageTwin –WinGX and Crystals suites link seamlessly into ROTAX (by Simon Parsons and Bob Gould)

Lachlan M. D. Cranswick Slide 63 “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 – 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: 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: –FOX:

Lachlan M. D. Cranswick Slide 64 “Specialised and Commercial” Structure Solution Programs ZEFSA II – for Zeolites (GPL’d) – Focus – for Zeolites – 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: –Crystal Structure Determination Package (WinCSD/CSD) : –DASH (Druid and Mystic of old): –TOPAS : –Endeavour :

Lachlan M. D. Cranswick Slide 65 EXPO direct methods in Action (1 of 4) Edit the input / control file

Lachlan M. D. Cranswick Slide 66 EXPO direct methods in action (2 of 4) Click on the OK button to start

Lachlan M. D. Cranswick Slide 67 EXPO direct methods in action (3 of 4) Le Bail fitting of the powder pattern

Lachlan M. D. Cranswick Slide 68 EXPO direct methods in action (4 of 4) Structure after being solved and auto built

Lachlan M. D. Cranswick Slide 69 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 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 Range of programs to choose from:

Lachlan M. D. Cranswick Slide 70 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?)

Lachlan M. D. Cranswick Slide 71 Shelxs direct methods (tetracycline hydrochloride) via WinGX as an interface

Lachlan M. D. Cranswick Slide 72 Sir direct methods and auto Fourier building (tetracycline hydrochloride) via WinGX as an interface

Lachlan M. D. Cranswick Slide 73 Dirdif Patterson methods and auto Fourier building (tetracycline hydrochloride) via WinGX as an interface

Lachlan M. D. Cranswick Slide 74 Crunch for UNIX direct methods and Fourier building (tetracycline hydrochloride) via Platon/System S as an interface

Lachlan M. D. Cranswick Slide 75 2D to 3D model building software Applicable for Generating 3D fragments for Patsee/Dirdif Orient – single crystal/powder Summary list at: – E.g., CORINA (COoRdINAtes) (Use web based direct submission): 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)

Lachlan M. D. Cranswick Slide 76 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 – 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

Lachlan M. D. Cranswick Slide 77 Single Crystal Structure Refinement Software (Applicable to powder diffraction for helping build up the structure) Range of programs to choose from: – 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)

Lachlan M. D. Cranswick Slide 78 Example of Crystals for Windows David Watkin, Richard Cooper, et al.: Will focus on Guided refinement

Lachlan M. D. Cranswick Slide 79 Guided structure refinement using Crystals Import Shelx INS file of structure solved by DIRDIF Asymmetric unit is always in view

Lachlan M. D. Cranswick Slide 80 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

Lachlan M. D. Cranswick Slide 81 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)

Lachlan M. D. Cranswick Slide 82 Guided structure refinement using Crystals Have now refined atom positions anisotropically Atoms can be displayed anisotropically

Lachlan M. D. Cranswick Slide 83 Guided structure refinement using Crystals Automatic Hydrogen Addition Graphically compare calculated hydrogens (white) to possible hydrogens found in the difference map (pink).

Lachlan M. D. Cranswick Slide 84 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.

Lachlan M. D. Cranswick Slide 85 Interrupt the Guided Refinement in Crystals Manual Hydrogen Addition - 2 of 2 A “Wizard” then guides the user to complete the hydrogen addition

Lachlan M. D. Cranswick Slide 86 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.

Lachlan M. D. Cranswick Slide 87 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

Lachlan M. D. Cranswick Slide 88 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

Lachlan M. D. Cranswick Slide 89 Validation using Crystals Cambridge database geometry check (2 of 4) Using the GUI (or scripts) make the offending Nitrogen a Carbon and re-refine.

Lachlan M. D. Cranswick Slide 90 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.

Lachlan M. D. Cranswick Slide 91 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.

Lachlan M. D. Cranswick Slide 92 Structure Refinement using Powder Diffraction Data (Rietveld Refinement) Large range of programs to choose from: – 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

Lachlan M. D. Cranswick Slide 93 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.

Lachlan M. D. Cranswick Slide 94 Rietveld Programs - Rietica by Brett Hunter  Full Graphical User Interface  Still got to appreciate and know your crystallographyfor inserting and refining the crystal structure 

Lachlan M. D. Cranswick Slide 95 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) – 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 Slide 96 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,

Lachlan M. D. Cranswick Slide 97 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.)

Lachlan M. D. Cranswick Slide 98 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

Lachlan M. D. Cranswick Slide 99 Restrained Rietveld structure refinement of organics Software not as powerful as single crystal but there are some tutorials with tricks on the CCP14 website

Lachlan M. D. Cranswick Slide 100 Fourier capability in Rietveld Software GSAS (including VRML output) Summary list of Fourier friendly Rietveld software at: Fullprof / GFOUR for Windows

Lachlan M. D. Cranswick Slide 101 Single Crystal Suites (also applicable to powder diffraction) Again, a large range of programs to choose from: – 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

Lachlan M. D. Cranswick Slide 102 WinGX for Windows single crystal suite Louis Farrugia: 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

Lachlan M. D. Cranswick Slide 103 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

Lachlan M. D. Cranswick Slide 104 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

Lachlan M. D. Cranswick Slide 105 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

Lachlan M. D. Cranswick Slide 106 WinGX for Windows single crystal suite Refinement - Shelxl 97 GUI control of Shelx via WinGX’s SXGRAPH program or Shelx ASCII INS File

Lachlan M. D. Cranswick Slide 107 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)

Lachlan M. D. Cranswick Slide 108 WinGX for Windows single crystal suite Easy Interlinking with Ton Spek’s Platon Squeeze/disordered solvent effects ADDSYM Other Platon Features

Lachlan M. D. Cranswick Slide 109 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

Lachlan M. D. Cranswick Slide 110 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

Lachlan M. D. Cranswick Slide 111 WinGX for Windows single crystal suite Validation and Structure Checking Platon (Addsym, etc) CIF Validation Parst GEOM THMA 14c IDEAL SYMMOL WTANAL R-tensor

Lachlan M. D. Cranswick Slide 112 Some Specialist Applications Charge Density (single crystal) –Project XD – Anharmonic Refinement –List of Software: – Incommensurate Structure Refinement –List of Software: – PDF / High Q Analysis –List of Software: –

Lachlan M. D. Cranswick Slide 113 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)

Lachlan M. D. Cranswick Slide 114 MAUD for Java : GPL’d (you get the source code) Tutorial on “Performing an x-ray quantitative analysis in seven easy steps!” :

Lachlan M. D. Cranswick Slide 115 Quantitative Phase Analysis - is it routinely easy? Based on the IUCr CPD Quant Round Robin ( The answer seems to be No! A quote from Armel Le Bail’s Tmacle “twinned refinement” manual seems appropriate: 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

Lachlan M. D. Cranswick Slide 116 Graphically interacting with the structure Number of programs available with list available at: 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 Bochu

Lachlan M. D. Cranswick Slide 117 Graphically interacting with the structure (more examples) GUI WinORTEP ( GUI WinSTRUPLO (

Lachlan M. D. Cranswick Slide 118 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!

Lachlan M. D. Cranswick Slide 119 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)

Lachlan M. D. Cranswick Slide 120 WinGX for Windows single crystal suite Validation and Structure Checking Platon (Addsym, etc) CIF Validation Parst GEOM THMA 14c IDEAL SYMMOL WTANAL R-tensor

Lachlan M. D. Cranswick Slide 121 Platon’s Addsym (by Ton Spek): checking for extra symmetry : e.g., Structure Published in 1997 P1 - Triclinic: 42 non-H atoms

Lachlan M. D. Cranswick Slide 122 Platon’s Addsym: Correction Published in 1999: C2 - Monoclinic: 22 non-H atoms

Lachlan M. D. Cranswick Slide 123 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)

Lachlan M. D. Cranswick Slide 124 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 –addsym gives P 2/c and exact fit on Pc Loosening defaults: –calc addsym shelx exact –P-31m

Lachlan M. D. Cranswick Slide 125 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!

Lachlan M. D. Cranswick Slide 126 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

Lachlan M. D. Cranswick Slide 127 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

Lachlan M. D. Cranswick Slide 128 Powder diffraction pattern calculation Poudrix for Windows Powder Cell by Jean Laugier and Bernard Bochu Poudrix can handle anomalous dispersion at non X-ray tube wavelengths with the option of two models: –Brenann and Cowan –Sasaki

Lachlan M. D. Cranswick Slide 129 Photorealistic hardcopy output of structures Many programs can do this. E.g, ORTEX (Images and Movie Animations): Just open up a Shelx format *.INS/*.RES file and go for it

Lachlan M. D. Cranswick Slide 130 Photorealistic hardcopy output of structures GUI WinORTEP / GUI Struplo / WinGX Can open a wide variety of file formats including Shelx, CIF, GSAS, Fullprof, CDS, etc

Lachlan M. D. Cranswick Slide 131 Photorealistic hardcopy output of Fourier Maps Marching Cubes by Michal Husak ( Interlinks with WinGX, Crystals and can read Project XD files.

Lachlan M. D. Cranswick Slide 132 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: FreeBSD (can run linux binaries) –refer: (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 (Supported & Sponsored by the IUCr and CCP14) Contact the author (Lachlan Cranswick) for a free air-mailed CD-ROM.

Lachlan M. D. Cranswick Slide 133 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: