Introduction

Crystal Structure Databases

Indexing/Spacegroup Assignment

Absorption Correction Options

Structure Solution

Structure Refinement

Single Crystal Suites

Graphically Interacting with the Structure

Fourier Map Generation and Viewing

Structure Quality Checking

Exporting/Importing CIF files

Specialised Programs

Structure Visualisation and Photorealistic Hardcopy Output

Solving Structures using Powder Diffraction

Utilities/Resources/PC Operating Systems

Thus these notes with all the web links are on the web at:

http://www.ccp14.ac.uk/poster-talks/bca200/

Aim to try and give a feel for what is available but also what it is like to install and use many of the programs.

(by default, most of the windows programs install using a friendly setup.exe installer)

Software that is freely available via the internet is emphasized even though others do exist and should also be investigated for those looking into building up their crystallographic toolkits:

NRCVAX

Like Xtal Suite – a Collaborative Community Effort.

(possibly available freely on the web soon(?))

E-mail Peter White ([email protected])

XSEED:

http://www.lbarbour.com/xseed

(US$ 1,000 for a site license)

B.A. Frenz SPD Single Crystal Suite

http://www.bafrenz.com

(US$ 995 for Academic Site License)

Hardware vendor based Single Crystal Software

If you are happy with the software you are presently using – why bother looking into alternatives?

Researchers are most at risk from not knowing what they do not know.

It is important to have access to a wide "genetic diversity" of software to handle wide variety of structure problems in the most effective manner. (for both the expert and part time crystallographer)

There is a "good" genetic diversity of freely available single crystal structure solution and refinement programs that can enabled both expert and "part time crystallographers" in tackling a wide diversity of structural problems.

To enable fast download, where possible, software is mirrored at the CCP14 project web site via in the UK:

http://www.ccp14.ac.uk

and regional mirrors

(presently in Australia and Canada).

Much newly released, freely available software have high quality "point and click" Graphical User Interfaces by default.

Freely available GUI Single Crystals SUITES are now becoming available and are extremely powerful in the manner that many crystallographic utilities are linked together with multiple pathways for solving and refining a structure. Thus no need for tedious manual file handling when passing between programs.

(ORTEX, WinGX, System S, GNU Xtal, CRYSTALS)

Crystal Structure Databases

If you are a student or academic working in the UK, you have free access (via National Licences) to all the main Crystal Structure Databases via the EPSRC funded Chemical Database Service (CDS). You can register (no charge) at:

http://www.dl.ac.uk/CDS/cds.html

Single Crystal Indexing/Spacegroup Assignment

Most hardware vendors provide options for indexing but there are free-standing programs that can provide other options.

DIRAX for difficult Indexing problems.

ftp://ftp.chem.uu.nl/pub/dirax/

ABSEN Single Crystal Program by Patrick McArdle

(comes with the ORTEX and WinGX suites)

Indexing, spacegroup reasignment options within Platon/System S by Ton Spek for pre and after structure solution/refinement spacegroup assignment.

(Windows users: Platon is included with WinGX or can be run free standing)

Absorption Correction Options

Ortex, Crystals, WinGX and Platon give access to a variety of Absorption correction options.

Viewing or HKL Profiles

Blessing DREAR Software

Numerical:

Semi-Empirical:

Psi-scans, Camel-Jockey, Multiscan

RefDelF:

Difabs, XABS2, Shelxa

Platon

(Has the option of Viewing the Crystal Habit)

Single Crystal Structure Solution

CAOS (also inside part of Sir97) – Ricardo Spagna, et. al.

Comes with an automatic Patterson Solution Option.

http://www.org.chemie.uni-frankfurt.de/egert/patsee.html

http://www.ccp14.ac.uk/ccp/web-mirrors/patsee/egert/patsee.html

Crisp – Part of the GNU Xtal Suite

Direct Methods

http://xtal.crystal.uwa.edu.au/

http://www.ccp14.ac.uk/ccp/web-mirrors/xtal/

Crunch – R. de Gelder, R.A.G. de Graaff & H. Schenk,

Direct Methods and automatic structure building

http://www-xtal.sci.kun.nl/xtal/documents/software/crunch.html

http://www.ccp14.ac.uk/ccp/web-mirrors/dirdif/xtal/documents/software/crunch.htmL

Dirdif - P.T. Beurskens, G. Beurskens, R. de Gelder, et al.

http://www-xtal.sci.kun.nl/xtal/documents/software/dirdif.html

http://www.ccp14.ac.uk/ccp/web-mirrors/dirdif/xtal/documents/software/dirdif.html

http://www.ccp14.ac.uk/ccp/web-mirrors/farrugia/~louis/dirdif/

Patsee – E. Egert and G. Sheldrick

Fragment Search

http://www.org.chemie.uni-frankfurt.de/egert/patsee.html

http://www.ccp14.ac.uk/ccp/web-mirrors/patsee/egert/patsee.html

Single Crystal Structure Solution (cont’d)

Shake’n’Bake (SnB) – Weeks, Miller, et al.

Dual-space direct methods. (Linux, SGI, Alpha executables via web)

http://www.hwi.buffalo.edu/SnB/

Shelxs 86/97- George Sheldrick

Direct Methods and Patterson Option

http://shelx.uni-ac.gwdg.de/SHELX/index.html

Sir92/97 – Sirware Group: Cascarano, Giacovazzo el al

http://www.ba.cnr.it/IRMEC/SirWare_main.html

http://www.ccp14.ac.uk/ccp/web-mirrors/sirware/IRMEC/SirWare_main.html

Solver – in NRCVAX Suite – based on Multan

Direct Methods

Peter White ([email protected])

XFPA – Frantisek Pavelcik

Patterson Methods and automatic structure building

E-mail: [email protected]

Shelxs97 direct methods:

http://shelx.uni-ac.gwdg.de/SHELX/index.html

Resulting structure ready for building up:

Sir97 direct methods:

(Sir2000 is on the way – aim for handling difficult problems with more than 2000 atoms in the asymmetric unit)

http://www.ba.cnr.it/IRMEC/SirWare_main.html

http://www.ccp14.ac.uk/ccp/web-mirrors/sirware/IRMEC/SirWare_main.html

Here Sir97 is just at the point of automatically assigning atom types during the automatic building up of a structure:

After Completion (just have to rename 3 atoms):

Dirdif solving a Structure. Program of choice for heavy atom problems.

http://www-xtal.sci.kun.nl/xtal/documents/software/dirdif.html

http://www.ccp14.ac.uk/ccp/web-mirrors/dirdif/xtal/documents/software/dirdif.html

Windows: http://www.chem.gla.ac.uk/~louis/dirdif/

http://www.ccp14.ac.uk/ccp/web-mirrors/farrugia/~louis/dirdif/

Resulting structure with every assigned non-Hydrogen atom correctly placed and named:

Structure solved (via System S) and built to near completion (though this is really a heavy atom problem). One missing Carbon atom and various atom reassignments to be done.

(As shown via System S/Platon suite)

http://www-xtal.sci.kun.nl/xtal/documents/software/crunch.html

http://www.ccp14.ac.uk/ccp/web-mirrors/dirdif/xtal/documents/software/crunch.htmL

CRUNCH does get some bad comments based on it reportely crashing UNIX workstations.

Personally have found CRUNCH to have a robust and problem free UNIX install/compile/usage.

When crunch installer script asks for how much RAM you should give to Crunch,

can be a bad idea to state more physical RAM that you really have.

i.e., if you have 64 Meg RAM, state that Crunch can have 48 Meg.

Giving more RAM than physically available (with exception of FreeBSD and Digital UNIX) is great way to grind/crash the UNIX system to death. (near guaranteed to crash/freeze up SGI IRIX)

Tutorial Install: http://www.ccp14.ac.uk/tutorial/crunch/

(Linux, SGI and Alpha Executables available at present)

http://www.hwi.buffalo.edu/SnB/Availibility_snb_V2.htm

.

To extract the files, type gzip –d < filename.tar.gz | tar xvof –

Type Install to install (example from an SGI O2)

(Linux Java can be problematic – Dec 1999)

For Cshell, in the .cshrc

set path=(/snb_binary_directory $path)

do source .cshrc then rehash commands

And good times are now yours.

Running SnB (type SnB)

Java GUI Interface will then take you through setting up SnB up to visualising resulting structures. Though is not for those who like speedy results. Think "weeks/months" in computational time for large structures.

Difficult Structures/Collaborating with Software Authors

By default many difficult structures may not solve and/or show up problems with existing software. Obvious solution is to pass this on to structure solution software authors to help "train up" their programs:

(Not sure how many people are into this habit?)

Cyclodextrin with guest molecules.

Cell ~30 x ~30 x ~30. > 1000 atoms in the asymmetric unit

Installing System S with Crunch and Sir97 on an SGI O2 shows up problems/bugs with both direct methods programs. (Reported to authors)

Shake n Bake on SGI O2 = into its 40^th trial after 2 weeks. Last heard: was still on the case (4 weeks later).

Within 2 weeks: Sir fixed and structure solved with Sir2000 in default mode. (expected release of Sir2000 at ECM 2000 meeting in Nancy)

2D-3D Model Building Software

(Applicable for Generating 3D fragments for Patsee/Dirdif Orient)

For a list, refer:

http://www.ccp14.ac.uk/solution/2d_3d_model_builders/

E.g., CORINA (COoRdINAtes):

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:

(Recommend using the "Direct Submission" option for immediate resulting MOL file, not the batch submission)

New WinGX "SXGRAPH" GUI Shelx INS/RES file Editor

(In the following case, a Cyclodextrin Fragment)

Single Crystal Structure Refinement

Shelxl (refinement program for System S/ORTEX/WinGX)

http://shelx.uni-ac.gwdg.de/SHELX/index.html

Crystals

http://www.xtl.ox.ac.uk/

http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/crystals/pub/crystals/

CAOS (freestanding and also available inside Sir97)

http://www.isc.mlib.cnr.it/caos/

http://www.ccp14.ac.uk/ccp/web-mirrors/caos/caos/

http://www.ba.cnr.it/IRMEC/SirWare_main.html

http://www.ccp14.ac.uk/ccp/web-mirrors/sirware/IRMEC/SirWare_main.html

GNU Xtal

http://xtal.crystal.uwa.edu.au/

http://www.ccp14.ac.uk/ccp/web-mirrors/xtal/

(NRCVAX – Contact: [email protected])

Some more specialised examples:

JANA

http://www-xray.fzu.cz/jana/jana.html

http://www.ccp14.ac.uk/ccp/web-mirrors/jana/jana/jana.html

Incommensurate and f’ f’’ refinement

GSAS

ftp://ftp.lanl.gov/public/gsas/

http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/

Combined powder/single crystal. f’ f’’ refinement.

Fullprof (is included with Winplotr graphics program)

ftp://bali.saclay.cea.fr/pub/divers/winplotr/

http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/fullprof/pub/divers/winplotr/

Combined powder/single crystal. Incommensurate structures.

Example of Sir97/CAOS:

By default, CAOS is used via a powerful scripting language. It is more Photogenic when operated inside Sir97 (point and click mode) thus the following screen dumps are from Sir97

Deleting, re-naming, re-sorting, etc at the click of a button.

Automatic Addition of Carbon bonded hydrogens at the click of a button:

GUI CRYSTALS for Windows:

Guided refinement of a crystal structure including automatic hydrogen addition.

Overlay of calculated and found hydrogens for high quality hydrogen placement:

Restraints and Constraints defined by selecting atoms using point and click of the mouse:

Single Crystal Suites

Single crystal suites can be extremely powerful as they allow users to quickly pick and mix a variety of programs at the click of a button.

ORTEX - Patrick McArdle

Shelx86/Shelxs97 for Structure Solution

Shelxl for refinement

http://www.nuigalway.ie/cryst/

http://www.ccp14.ac.uk/ccp/web-mirrors/ortex/cryst/

WinGX - Louis Farrugia

Shelxl for refinement

http://www.chem.gla.ac.uk/~louis/software/

http://www.ccp14.ac.uk/ccp/web-mirrors/farrugia/~louis/software/

System S/Platon - Ton Spek

Shelx86/Shelx97, Sir97, Dirdif, Crunch Structure Solution

Shelxl for refinement

http://www.nuigalway.ie/cryst/

http://www.ccp14.ac.uk/ccp/web-mirrors/ortex/cryst/

Crystals – David Watkin, Prout, Carruthers, Betteridge, Richard Cooper

Shelxs97 and Sir92/Sir97 for Structure Solution

Crystals for refinement

http://www.cryst.chem.uu.nl/platon/

http://www.ccp14.ac.uk/ccp/web-mirrors/platon-spek/platon/

3 Separate Least Squares Refinement Programs within GNU Xtal

http://xtal.crystal.uwa.edu.au/

http://www.ccp14.ac.uk/ccp/web-mirrors/xtal/

NRCVAX – Peter White (E-mail: [email protected])

Solver for Structure Solution – others link in. NRCVAX for Refinement,

Properties of the Single Crystal Suites

Note: It is almost impossible to do justice to any of these single crystal suites withing the time allowed.

You can be guided through the structure solution and refinement.

But you are not straight jacketted and can define your own route through the structure solution and refinement. It is entirely up to your personal preferrences and likes. And you can go between the suites if you wish

E.g.,

Face Index Absorption Correction using WinGX/Platon

Spacegroup analysis via ORTEX

Solving via WinGX

Building via System S/Platon

Refinement and Hydrogen placement in Crystals or GNU Xtal

Rendering photorealistic images via ORTEX

Can save hours in manual file handling in going between different programs.

WinGX/ORTEX/System S/Shelx/CAOS/GNU Xtal/Crystals - all have their own nuances and strengths for interacting with the structure and data. This variety is not a bad thing as you can gain insights into the structure nuances/data quality via these differing routes.

Single Crystal Suites Interfaces

ORTEX:

WinGX:

Platon/System S:

Crystals:

Example of the GNU Xtal Suite

Using the PIG (Portable Interactive Graphics) Interface

Non-Trivial Structure Solution of an Inorganic made Trivial using WinGX

(Note: there is a difference between a program’s ability to solve a structure and a person’s ability to use a structure solution program)

WinGX gives access to 6 structure solution programs at the click of a mouse button.

Structure solved and auto-builds to completion

Multiple Pathways for Structure Solving

Solving in one program – automatic building in another – via System S

(Again, Cesium Titanium Silicate)

Solve in Shelx86

Use the System S/Platon EXOR function to build up the structure

(also have the other options of using Crunch, Sir and Dirdif to build up the structure).

One oxygen atom left to find (after refining heavy atoms anisotropically). Purple Q peak stands out quite clearly.

Graphically Interacting with the Structure

Most freely available programs and suites now have the ability to interact directly with a graphical representation of the structure during solving and refining.

For routine and not so routine refinements, point and click interfaces are now available, complementing the ASCII file or command line interfaces.

Fourier Map Generation and Viewing

With suites such as WinGX, Platon/System S. Xtal and Crystals, it is trivial to generate Fourier Contour Maps for detailed viewing and analysis.

WinGX:

The WinGX suite has many strong points and one is it’s Fourier Map generation and viewing utilities.

In the above Cesium Titanium Silicate, thermals on one or two of the oxygens seem quite large. If you don’t believe your eyes, a check through Platon will tell you about it.

Doing an Shelxl OMIT on the offending atom, go into the WinGX Fourier Map Generator tpo generate a difference map (either slant plane of 3D):

Generate the map:

Animating through the map, it is possible to see a slight peanut shape in the difference map of the oxygen showing a slight split atom problem.

Example of WinGX fourier map animating through a zeolite with disordered template.

Crystals – Slant Plane Fourier Map:

Define the Slant Plane by selecting 3 atoms then right click to go into the Fourier Map option.

Examine slant plane difference map looking at hydrogen positions – via the Marching Cubes 3D Fourier Map viewer by Michal Husak (also linked into WinGX – and potentially any other program that supports the formats Marching Cubes recognises)

http://mysak.umbr.cas.cz/~husakm/Public/MarchingCubeELD/MarchingCubeELD.htm

http://www.ccp14.ac.uk/ccp/web-mirrors/marchingcube-fourierviewer/~husakm/Public/MarchingCubeELD/MarchingCubeELD.htm

Platon/System S Fourier Map:

Examining slant plane difference map looking at hydrogen positions.

Using WinGX MapView:

(Can be run as a freestanding program linked into any program that will output a Mapview friendly format)

Examining slant plane difference map looking at hydrogen positions

Using the 2D Bitmap Mode of MapView:

Structure Quality Checking

(Each suite can offer different features)

ORTEX:

Example of the Void Finding and graphical viewing within ORTEX (including estimate of time to completion)

Structure Quality Checking

WinGX:

Links to a wide variety of Structure Checking, Analysis Options and Utilities (including a Windows version of Platon).

GUI XHYDEX (GUI over code by G. Orpen): Searching for Likely hydrogen positions. GUI CALC-OH (Nardelli 1999) GUI Parst, GUI Model and Data Transformation, SG Info, etc, etc.

Platon:

Structure checking options such as: Addsym, newman, etc.

Automatic Generation of a Quest Script (and automatically spawn quest if applicable) to see if structure has already been determinated or check out related structures:

Specialist Applications

Charge Density

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

Exporting/Importing CIF files

Importing to a useful crystallographic format can be a problem.

http://www. iucr.org/iucr-top/cif/

Source Code (and DOS executable): CIF2SX by Louis Farrugia

http://www.chem.gla.ac.uk/~louis/software/

http://www.ccp14.ac.uk/ccp/web-mirrors/farrugia/~louis/software/

Windows: WinGX by Louis Farrugia

using the "Model, Import, CIF File" menu option

http://www.chem.gla.ac.uk/~louis/software/

http://www.ccp14.ac.uk/ccp/web-mirrors/farrugia/~louis/software/

UNIX: Platon/System S by Ton Spek

using the "s filename.fcf" command line.

http://www.cryst.chem.uu.nl/platon/

http://www.ccp14.ac.uk/ccp/web-mirrors/platon-spek/platon/

UNIX: Platon/Pluton – Ton Spek

Windows: Ortep-3 – Louis Farrugia (or WinPlaton)

Structure Visualisation and Photorealistic Hardcopy Output

Examples of Software that can do this:

(problem can be that or having a high enough quality printer)

ORTEX (Rendoring and Animation):

http://www.nuigalway.ie/cryst/

http://www.ccp14.ac.uk/ccp/web-mirrors/ortex/cryst/

Just open up a Shelx format *.INS/*.RES file and go for it

http://www.chem.gla.ac.uk/~louis/software/

http://www.ccp14.ac.uk/ccp/web-mirrors/farrugia/~louis/software/

Can load a variety of structure formats including some Rietveld formats such as GSAS, LHPM, Fullprof, Rietan.

Platon

http://www.cryst.chem.uu.nl/platon/

http://www.ccp14.ac.uk/ccp/web-mirrors/platon-spek/platon/

GNU Xtal Suite

http://xtal.crystal.uwa.edu.au/

Dual Boot UNIX/Windows PCs

Get the ability to run a very wide range of crystallographic software on cheap, powerful commodity PCs.

Easy to say this is easy after spending a month or so working it out.

CCP14 based tutorials on installing multi-boot

Free UNIX Operating Systems (install off the internet)

Linux

refer: http://www.ccp14.ac.uk/solution/linux/

FreeBSD (can run linux binaries)

refer: http://www.ccp14.ac.uk/solution/bsdunix/

http://www.vmware.com/

(Commercial software)

Freely Available Compilers, GUI Building Kits and Source Code

http://www.ccp14.ac.uk/recomm/

Solving Structures Using Powder Diffraction Data

Highly non-trivial compared to single crystal.

You may be lucky to get beyond correctly indexing the powder data and obtaining a cell.

You might also find that Powder Diffraction Rietveld Structure Refinement software is around 5 to 20 years behind in usability, interaction and robustness compared to single Crystal Equivalents such as Shelx, Crystals, CAOS, Sir97, GNU Xtal and the Single Crystal Suites.

This is not to say that Rietveld refinement programs are not any good. It is mainly an indicator on how powerful modern single crystal programs have become in dealing with large and complex structures.

Solving Structures Using Powder Diffraction Data

Some Links

Powder Data Conversion:

http://www.ccp14.ac.uk/solution/powderdataconv

Search-Match/Phase Identification:

http://www.ccp14.ac.uk/solution/search-match.htm

Powder Indexing

http://www.ccp14.ac.uk/solution/indexing/

Unit-cell Refinement:

http://www.ccp14.ac.uk/solution/unitcellrefine/

LeBail Method for Intensity Extraction

http://www.ccp14.ac.uk/solution/lebail/

Pawley Method for Intensity Extraction

http://www.ccp14.ac.uk/solution/pawley/

Powder Diffraction Structure Solution Pathways

Available Rietveld Software

If you see too many software options, feel free to E-mail the CCP14 ([email protected]). Pros and cons of various software can depend on the structure type.

Example Powder Indexing and Spacegroup Assignment

"Crysfire" Indexing Suite

(ito, treor, dicvol, taup, lzon, fjzn, losh and kohl)

http://www.ccp14.ac.uk/tutorial/crys/

(Reads a CRYSFIRE *.SUM summary file)

http://www.ccp14.ac.uk/tutorial/lmgp/

Example of Unsolvable cell on powder data made routine by not relying on "favourite" programs.

Favourite program here was to use Treor by itself and ASCII output file. Highly non-trivial to impossible.

Made Routine by combination of CRYSFIRE (incorporating Treor) and Chekcell – despite reporting of the cell by Ito indexing program as orthorhombic a=c

Example Structure Solving from Powder Diffraction

(sequel to Sirpow – Sir97 for Powder Diffraction)

http://www.ba.cnr.it/IRMEC/SirWare_main.html

http://www.ccp14.ac.uk/ccp/web-mirrors/sirware/IRMEC/SirWare_main.html

Downloading of Software

The above software and resources can be downloaded via the CCP14 site:

If any queries, E-mail:

[email protected]

or:

[email protected]

Graphical tutorial run-throughs of most of this software is located via ("look before you try"):

Software is installed on the CCP14 laptop for demonstration at any time during this meeting.

Where allowed, can be installed on any local computer for demonstration.