A structure is not truly solved until it is refined! : tricks and hints for using Alan Larson and Bob von Dreele's GSAS, and Brian Toby's EXPGUI, for combined

A structure is not truly solved until it is refined! : tricks and hints for using Alan Larson and Bob von Dreele's GSAS, and Brian Toby's EXPGUI, for combined X-ray / Neutron refinement and restrained Rietveld refinement of large polymeric inorganics and minerals.

Lachlan M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for

Single Crystal and Powder Diffraction)

Department of Crystallography;

Birkbeck College, University of London,

Malet Street, Bloomsbury, London, WC1E 7HX, UK.

E-mail: [email protected]

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

AGU 2002: “hints and tricks for using GSAS Rietveld”Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk

Slide 2

Notes Free Zone - they are on the web

http://www.ccp14.ac.uk/poster-talks/agu2002b/


Slide 3

Talk Aims

• Provide hints on performing restrained Rietveld refinement of large inorganics using GSAS including:

– Data conversion

– Histogram weighting

– Charge Balance Restraints

– Total cell composition restraints

– Bond length restraints

– Bond angle restraints

– Using Platon and WinGX to help validate the structure


Slide 4

Topics Discussed

• Converting Madsen and Hill VCT data and x,y,weight column data into GSAS format

• Using Brian Toby’s EXPGUI as a primary interface into GSAS

• Hints on using GSAS for combined X-ray / Neutron refinement

• Hints on GSAS Rietveld for restrained refinement of large inorganic polymeric framework structrures

• Using macros in GSAS


Slide 5

An initial point - computer skills

• When doing complicated (and not so complicated crystallography and powder diffraction), it is assumed the user has good general computer skills.– General program installation and configuration

– Good text editing skills

– Having multiple programs open and interacting between them

– Cut and paste using both mouse and keyboard speed keys.


Slide 6

GSAS

• by Bob von Dreele and Alan Larsen - ftp://ftp.lanl.gov/public/gsas/

• CCP14 based resources:– http://www.ccp14.ac.uk/solution/gsas/

• What may look like minor changes can result in ability to handle what were intractable problems.


Slide 7

GSAS: 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

• 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


Slide 8

Brian Toby’s EXPGUI Interface for GSAS

User friendlier to start using GSAS via EXPGUI(A new combined installer makes it very easy to start using GSAS.)

http://www.ncnr.nist.gov/programs/crystallography/software/expgui/expgui_intro.html


Slide 9

Brian Toby’s EXPGUI: Easy to start a new refinement (1 of 13)

• Run EXPGUI and go to the required directory and enter a new filename (in this case pbso4) and press “read”. When prompted, then press the “Create” icon


Slide 10


• When prompted, enter an experimental title then press the “Set” icon.


Slide 11


• Click on the “Phase” tab and then the “Add Phase” Icon. Input the cell and spacegroup information


Slide 12


• Click “Add” then “Continue” to the cell and spacegroup information to be incorporated into GSAS.


Slide 13


• Click “Add New Atoms” and add in the starting model either by hand or importing a PowderCell format file.


Slide 14


• Click “Add Atoms” to get the starting model into GSAS


Slide 15


• Set appropriate damping factors (I tend to like somewhere between 7 and 9)

• (Lessen damping factors if parameter shifts are too small)


Slide 16


• Add the first XRD diffraction file: Select “Histogram” tab then “Add New Histogram” icon.


Slide 17


• Via the GUI, select the data file and the instrument parameter file. (in this case an XRD data file)


Slide 18


• Click “Add” to add the XRD file into GSAS. Change the damping factors and fix up any incorrect diffractometer constants (I.e., the parameter file may have incorrect information in it)


Slide 19


• It is easy to add another data file. Select the “Add New Histogram” icon. (select the Bank number if this is relevant)


Slide 20


• Click “Add” to add the second XRD file into GSAS. Again, change the damping factors and fix up any incorrect diffractometer constants (I.e., the parameter file may have incorrect information in it)


Slide 21


• Now you are ready to run Powpref and Genles and start refining the various “relevant” parameters

• Under Profile, Powder XRD data might be happier being fitted with a type 3 profile function:– pseudo-Voight with Finger Cox Jephcoat peak asymmetry correction

• One extra hint for Bragg-Brentano XRD users - sample displacement parameter is “shft” in the profile options (can be preferable to use this instead of “zero offset”)


Slide 22

Brian Toby’s EXPGUI: Profile Screen in EXPGUI with shft


Slide 23

New(ish) Features in Brian Toby’s EXPGUI

• Graphically define the background

• Graphically exclude regions

• Can export structures to Platon format (Addsym, etc)


Slide 24

Brian Toby’s EXPGUI: Graphically Defining the Background (1 of 3)

• After powpref, select “powder, bkgedit” and use point and click with the mouse to select background points


Slide 25


• Use the Fit icon to fit a Chebyshev function through the data points - increase number of terms as required


Slide 26


• Save into EXP file. Background is now fixed but can be refined at the click of a button. Done.


Slide 27

Brian Toby’s EXPGUI: Graphically Excluding Regions (1 of 3)

• After powpref “and” genles (0 cycles just to perform a “calculation”), select “powder, excledt”


Slide 28


• Point and click to select excluded regions


Slide 29


• Run powpref and genles for this to take effect


Slide 30

Brian Toby’s EXPGUI: If things go beserk: Backtracking through previous runs to when before things went beserk.

• Select “File, Open” and the “Include Archived Files”


Slide 31

GSAS and example ceramic / polymeric inorganic problem

In this example, a perovskite based ceramic relevant to the wireless communications and the mobile phone industry (High Q ferroelectric)

–>120 atoms in R3

–>320 atoms in C1

– 54 possible “split occupancy” framework metal sites

– 54 possible atom / vacancy interstitial sites

– 162 oxygen sites

– >1600 bond restraints

– >200 atom constraints

– >150 atoms linked within a single constraint


Slide 32

GSAS and example ceramic / polymeric inorganic problem: chronic peak overlap

• Structure is Pseudo Cubic

– a=b=c= 23.9 Å

– Chronic peak overlap

– No non-overlapping reflections

• Screen image from EXPGUI shows some HKLs matching to some “LOW ANGLE” peaks.– Shift Left mouse button

in Expgui’s Liveplot


Slide 33

Will be concentrating on HOW to using GSAS for this type of problem

• Often hear that a program can handle a problem.• But often is not obvious or obscure how to go about

using a program.• This will be concentrating on the “HOW”.• Structure is presently unpublished and only 99.9%

finished• Ian Grey of CSIRO Australia or Bob Roth of NIST

USA would be more appropriate to talk about the crystal chemistry and the structure itself.


Slide 34

Nuances and People Involved in this structure• Lead by Ian Grey (CSIRO, Melbourne Australia) and Bob Roth (NIST, Gaithersburg, USA)

• Synthesis: Bob Roth and Julia Chan (NIST, Gaithersburg) (is ~3 months of work and furnace time to synthesize a decent size batch of sample)

• TEM: Igor Levin (NIST, Gaithersburg) (looks like microdomain twinning problems)

• Single Crystal Work: Gus Mumme and Ian Grey (CSIRO, Melbourne) (looks like microdomain twinning problems)

• Powder Indexing / Le Bail fitting for looking at cell and spacegroup: Lachlan Cranswick (done at Columbia University) (Crysfire/Chekcell/Rietica)

• Structure Solution: Ian Grey and Gus Mumme (CSIRO, Melbourne)

– Atom Ordering: Gus Mumme and Ian Grey (CSIRO, Melbourne)

– Tilt Model: Ian Grey and Gus Mumme (CSIRO, Melbourne)

– Basic structure from chemical crystallographic arguments

– Starting atom ordering model from Shelxl and CSRIET structure refinement

– (Complex tilt model obtained from refining the perovskite subcell and looking at the Fourier difference map for peaks giving an indication of tilt directions and magnitudes)

• GSAS Structure Refinement: Lachlan Cranswick (done at Columbia University)

• New single crystal work based on GSAS Refined structure: Ian Grey and Pierre Bordet


Slide 35

Is GSAS the only effective program for large restrained inorganic Rietveld Refinements(?)

• Ability to handle very large arrays not the only issue• Controllable - via a menu / scripting system amenable

to scripting and automation• Large variety of restraints• Restraints can be disabled but still used for diagnostic

purposes• Can easily disable/enable restraints and histograms

(cyclic refinement instead of combined X-ray / Neutron refinement)


Slide 36

GSAS : YES! - at present the only effective Rietveld system for these types of large problems

• GSAS (by the Anna Karenina principle - a happy family):

• Can handle large numbers of atoms and restraints

• Large variety of restraints

• Menu based control amenable to scripts and automation

• Easy enabling and disable of histograms

• Integrated Fourier map including peak search

• TOF Neutron / EDX as well

• Other Rietveld Programs affected by one or more of the following problems

• Cannot handle large numbers of atoms or restraints

• Don’t have many types of restraints

• Manual editing of ASCII files or GUIs that do not easily allow quick changes to large numbers of atoms

• Problematic enabling and disabling of restrains and histograms

• No integrated Fourier map generation and viewing

• Can only handle constant wavelength neutron and angular dispersive X-ray diffraction data.


Slide 37

GSAS - relevant newish features

• Weighting of individual histograms / powder patterns

• Larger arrays for atom constraints

• Larger arrays for total chemistry constraints

• Viewing of larger Fourier electron density contour maps

• Other misc. changes


Slide 38

GSAS scales up!: to the point of refining protein 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


Slide 39

GSAS: Individual Histogram Weighting

• You don’t always have a choice on data collection

• Thus may need to weight histograms (diffraction data) such that they are roughly of equal weighting


Slide 40

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 and setting restraints


Slide 41

GSAS: Individual Histogram Weighting (using 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 menus

– x !exit expedt

• Run Powpref for new weighting to take effect


Slide 42

GSAS: If you DON’T Use Histogram Weighting

X-ray 8.0% R(F**2) Neutron 28.1% R(F**2)


Slide 43

GSAS: If you DO Use Histogram Weighting

X-ray 8.3% R(F**2) Neutron 11.7% R(F**2)


Slide 44

GSAS: Atom shift limits(so that atoms cannot shift more than a define absolute amount (Å))

• Set via EXPEDT– y !backup

– l !least squares setup

– l !least squares controls

– a !atom shift limits

– 0.1 !set the max allowed atom shift (0.1 Å in this example)

– x x x !exit menus

– x !exit expedt


Slide 45

GSAS: Rod Hill and Ian Madsen VCT data collection

• If you do have a choice of data collection strategies for XRD - use variable count time (VCT)

• Commercial vendors partially to blame for only having obsolescent data collection options in their data logging software.

• Still may need to play with weighting of histograms for “fine” control of the combined refinement. VCT Fortran Source Code with references is available:

http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/csirominerals-anon-ftp/pub/xtallography/


Slide 46

VCT for Refinement (1 of 4)Variable Count Time data (as collected - CAD4 style)


Slide 47

VCT for Refinement (2 of 4)

Variable Count Time data (normalised as FCT)


Slide 48


Variable Count Time data (normalised as FCT)


Slide 49


Variable Count Time data (displayed as VCT)


Slide 50

Getting Madsen and Hill VCT data into GSAS ESD format

• Mark Bowden’s VCTCONV for DOS (runs on Windows)– Download: http://www.ceramics.irl.cri.nz/Convert.htm


Slide 51

Getting ASCII x,y,weight data into GSAS ESD format

• Using Nita Dragoe’s Powder v4 for Windows– (sequel to “Convert for Windows”)– Download via: http://www.ccp14.ac.uk/tutorial/powder/

• Open the x,y,z “free ascii” data

• Save as GSAS CW ESD format

• Done!


Slide 52

Setting up a Restrained Rietveld refinement of > 300 atom polymeric inorganic structures in GSAS

• Initial problem is setting everything up and the control of the refinement.

• But need the flexibility to change as you may only find new information while refining the structure. (change of spacegroup being the most obvious) – Eric Dowty’s shareware Cryscon can be very quick and effective for

transforming structures from one cell and spacegroup to another. http://www.shapesoftware.com/#anchor_cryscon

• One solution is to use a spreadsheet program that allows for flexibility and extendability (MS-EXCEL for Windows)


Slide 53

Restrained refinement in GSAS: setting up an EXCEL spreadsheet

• CCP14 based tutorial and example files at : http://www.ccp14.ac.uk/solution/gsas/restrained_inorganic.html

• Create GSAS script commands in EXCEL and save into txt MACRO files for importing into GSAS.

– (if applicable - model in arbitrary co-ordinates)

– Structure co-ordinates (if applicable - generated from previous model)

– Crystals (Watkin, Cooper, et al) structure co-ordinates for generating bond restraint lists for conversion by Scott Belmonte’s “coue” software into GSAS macro format.

• Crystals: http://www.xtl.ox.ac.uk/• Coue: http://www.ccp14.ac.uk/ccp/web-mirrors/scott-belmonte-software/

– Atom constraints

– Total cell contents and/or charge balance constraints

– If applicable, other scripts for controlling GSAS


Slide 54

GSAS: setting up an EXCEL spreadsheet: Example Atom Co-ordinates

• Calculate or import an atom list within Excel where it can be easily manipulated.

• In GSAS, you input the atom list via EXPEDT

– k l a

• Use Windows “cut and paste” or @r (import macro file command) while in the relevant menu


Slide 55

GSAS: setting up an EXCEL spreadsheet: ConTEXT freeware text editor and column editing

• The freeware ConTEXT editor can be very effective in getting bits of structure (or extracting HKL files) from text files using it’s “column editing” ability.– http://www.fixedsys.com/context/

• The column editor function is not on the menu but is called using [CONTROL] L. (cannot use the mouse for click and drag while in column editing mode - only the keyboard and arrow keys)


Slide 56

GSAS: setting up an EXCEL spreadsheet: Input for Crystals to generate GSAS bond restraints lists

• Just use EXCEL “=“ commands to copy over values from GSAS atom list

• Got to keep the atom numbers the same as GSAS atoms controls are based on the atom numbers

• Inputting bond length restraints in EXPEDT:

– k l s d

• More details given at:http://www.ccp14.ac.uk/solution/gsas/

restrained_inorganic.html


Slide 57

GSAS: setting up an EXCEL spreadsheet: Dual Occupancy Atom Constraints (in expedt: k l a k)

• Just copy and paste to extend the atom constraints to the desired number of atom sites. In this example for 108 atoms which would be painful to set up manually in GSAS.


Slide 58

GSAS: setting up an EXCEL spreadsheet: Total Cell Content Restraints (in expedt: k l s c)

• Extend as required depending on the number of atoms you wish to link into the constraint.

• The total number of atoms on the defined sites in this example is restrained to 81


Slide 59

GSAS: setting up an EXCEL spreadsheet: Charge Balance Restraints (in expedt: k l s c)

• Just use the Total Cell Contents Restraint which does not care what the value physically represent.

• To enforce charge balance just put the ionization value of each atom site - which should sum to zero.

• Simple example in the screen dump.

• The Total Chemistry Restraint will performs the sum calculation for you and tell you what the present sum is in the restraints menu.

• Even if you don’t use the restraint, inputting this can be a useful, quick check that you have charge balance.


Slide 60

GSAS: importing all these macro files into GSAS

• Copy the Excel cells to a TXT file.

• Use an Editor such as PFE to replace all “TABS” with “spaces”:

– http://www.ccp14.ac.uk/ccp/web-mirrors/pfe/people/cpaap/pfe/

• Use the @r - import macro file command while in the relevant menu

• Done!


Slide 61

GSAS: turning off /on histograms, restraints, atoms in EXPGUI

• Histograms can be turned on and off in Brian Toby’s EXPGUI via the “histogram” menu using “Set Histogram Use Flags” Icon.


Slide 62

GSAS: turning off /on histograms, restraints, atoms in EXPEDT

• Also can be done in GSAS’s EXPEDT

– k l s

– u - The use command

• e.g., turn off X-ray data (histogram 1), turn on bond restraints (histogram 2) and neutron data (histogram 3)

k l s ! Go into EXPEDT restraints menu

u 1 ! Use histogram 1 - X-ray Data

n ! No

u 2 ! Use histogram 2 - Bond Restraints

y ! Yes

u 3 ! Use histogram 3 - Neutron Data

y ! Yes

x x x ! Exit EXPEDIT menus and quit


Slide 63

GSAS: using restraints as diagnostics• Restraints don’t have to be enabled to exist inside GSAS

• Restraints can also be used diagnostically even if they are not enabled

• E.g., Charge Balance :

• Following screen dumps shows that the occupancies of the various metals are such that the total cell is out of charge balance.

– In EXPEDT: k l s c l ! last l is for list


Slide 64

GSAS: spiraling in on the minimum and final structure

• May have to refine in quite a spiral manner

• Initially - have found circular refinement to be more controllable than combined refinement to be more controllable

– heavy atoms using X-ray data

– Oxygens using neutron data

• Restraints - problem with cemented structure vs having the structure fall apart– If restraints cement the structure, turning off restraints; doing small numbers of

cycles and manually resetting errant atoms can get things rolling quite nicely.

– Relaxing restraints sometimes can improve the regular co-ordination. !?

• If structure goes haywire, it can be easier to start again from the initial model

• Wall paper bubble effect - tighten one errant atom causes 1 to 4 more to go out

• Be keen to exchange experiences on this


Slide 65

GSAS: lessening the tedium: batch file control of the refinement :

( fully ordered model)

– Combatting impatience - tedious refinement strategy– Can leave a strategy to run overnight

• (though you may suffer for this)• can be better to look after set periods of time and reset

wandering atoms - which can go walk-about even if constrained on a problematic refinement involving lots of pseudo-symmetry.

– Following examples for DOS / Windows (Linux / Unix is more flexible)

– The @m command can be used to log a command sequence to a file to server as the starting point for editing a custom macro file.


Slide 66

GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: script to increase the refined angular range)

• In this case setting up histogram 1 (powder XRD)

• File titled 70_2t_x.txt

• The BAT control file would then enabled (“use”) all relevant histograms and run powpref after this file before going through a genles run.

p ! powder setup

h ! histogram setup

e 1 ! edit histogram 1 (X-ray)

t ! set end of two theta

70 ! set 70 degrees

/ ! confirm this then exit

x

x

x

x


Slide 67

GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: changing the bond restraint weighting)

• File titled bondr10.txt

k ! don't make a backup of the file

l ! least squares

s ! soft constraints

d ! bond length restraints

f 10 ! set bond restr. weighting to 10

x ! exit expedt

x

x

x


Slide 68

GSAS: lessen the tedium: batch file control of the refinement :(EXPEDT Example: only refining on neutron data)

• File titled neuonly.txt

k

l ! least squares

s ! soft restraints menu

u 1 ! use histogram 1 - X-rays

n ! set to no

u 3 ! use histogram 3 - neutron

y ! set to yes

x

x

x


Slide 69

GSAS: lessen the tedium: batch file control of the refinement :(EXPEDT Example: refine heavy metal framework atoms)

• File titled

ref_fmh.txt


l ! least squares

a ! atom options

v 1:324 -x ! get rid of any X parameters refining

q ! quit atom list

v 1:324 -u ! get rid of any UISO parameters refining

q ! quit atom list

v 1:324 -f ! get rid of any FRAC parameters refining

q ! quit atom list

v 29:108 x ! set framework M sites refine on coords

q ! quit atom list

x

x

x


Slide 70

GSAS: lessen the tedium: batch file control of the refinement :(EXPEDT Example: refine light metal framework atoms)

• File titled

ref_fml.txt


l ! least squares

a ! atom options


q ! quit atom list


q ! quit atom list


q ! quit atom list

v 1:28 x ! set framework M sites refine on coords

q ! quit atom list

x

x

x


Slide 71

GSAS: lessen the tedium: batch file control of the refinement :(EXPEDT Example: refine interstitial metal atoms - less vacancies)

• File titled

ref_int.txt


l ! least squares

a ! atom options


q ! quit atom list


q ! quit atom list


q ! quit atom list

v 133:144 x ! set interstitial Met to refine



x

x

x


Slide 72

GSAS: lessen the tedium: batch file control of the refinement :(EXPEDT Example: refine oxygens)

• File titled

refoxy.txt


l ! least squares

a ! atom options


q ! quit atom list


q ! quit atom list


q ! quit atom list

v 163:324 x ! set oxygens to refine

q ! quit atom list

x

x

x


Slide 73

GSAS: lessen the tedium: batch file control of the refinement :(EXPEDT Example: refine UISO)

• File titled

refoxy.txt


l ! least squares

a ! atom options


q ! quit atom list


q ! quit atom list


q ! quit atom list

v 1:324 u ! set UISO of all atoms to refine

q ! quit atom list

x

x

x


Slide 74

GSAS: lessen the tedium: batch file control of the refinement :(Create a Batch File to follow your desired command sequence)

• File titled: refine.bat• In early stage of

refinement, a “cycle” of refinement involves:– Set bond restraint weight

– Enable only X-ray data

– refine framework metal atoms

– refine interstitial atoms

– Enable only Neutron data

– refine light oxygen atoms

– refine constrained UISO

• Batch files can be made more complicated with respect to logging what is happening

expedt model < batchjob\bondr1.txt

echo step 1 bond weight > autolog.txt

expedt model < batchjob\xrayonly.txt

echo step 2 XRAYS ONLY >> autolog.txt

expedt model < batchjob\ref_fhm.txt

genles model

echo step 3 completed >> autolog.txt

expedt model < batchjob\ref_flm.txt

genles model


expedt model < batchjob\neuonly.txt

echo step 5 NEUTRON ONLY >> autolog.txt

expedt model < batchjob\refoxy.txt

genles model


expedt model < batchjob\refuiso.txt

genles model



Slide 75

GSAS : If the refinement is not happy

• The tools are there for difficult refinements, but:– May not be easy!– May only find problems when in the middle of the refinement

• Impurities in many and varied forms

• XRD and Neutron data are different enough

– different impurities showing up

– different systematic effects

– different volumes of sample having their effect

• Wrong spacegroup

• Non-optimum atom ordering

• Non-optimum tilt model

• Extra elements in the sample - have you used a microprobe?


Slide 76

GSAS : “wall paper bubble effect trying to keep all bonds physically reasonable

• One problem trying to keep everything physically reasonable: trying to fix gives a “wall paper bubble effect” - fixed one bond causes 1 to 5 other bonds to become physically unreasonable.

• Suggestions on this appreciated (though this could be implying data purity problems)– Has been stated that the above can be a common

problem due to pseudo-symmetry and wrong spacegroup

– Though in this example looks like wrong chemistry and some octahedra really being tetrahedra


Slide 77

GSAS : Combined refinement on both XRD and Neutron in C1(bond length problems - “bubbles” - to stomp on)

(which imply problems with the model or symmetry).

X-ray 7.6% R(F**2)

(~3.8% R Bragg)

Neutron 4.2% R(F**2)

(~2.1% R Bragg)


Slide 78

Despite a good fit : model can still have problems : wrong chemistry was defined and structure not physically reasonable.

• In this case, GSAS refined model was used to try and determine twin laws on the single crystal data using “Jana” for refinement and Simon Parsons and Bob Gould’s “Rotax” (Fo/Fc) twinning software; and pre-defined twinning models.

• Refinement in R3 then C1 with and without various twin models gave a final R factor of 4.6%, untwinned in R3.

• Using the powder refined model as a starting point, it would seem that “Jana” was able to minimize on the single crystal data in R3 (and C1) where other programs possibly failed.


Slide 79

WinGX and Platon for validation of the structure and looking for higher symmetry

• EXPGUI can output Shelx INS and Platon SPF files.• Exporting a Shelx file can then be read by WinGX and

transferred to all its relevant callable programs– Structure plotting

– Geometry checking

– Platon


Slide 80

WinGX for Windows single crystal suite Validation and Structure Checking

• Platon (Addsym, etc)

• CIF Validation

• Parst

• GEOM

• THMA 14c

• IDEAL

• SYMMOL

• WTANAL

• R-tensor


Slide 81

Void checking using PlatonIn the case the pink balls are showing where significant voids are in located in the structure.


Slide 82

Graphically interacting with programs that are GSAS EXP file friendly

GUI WinORTEP (http://www.chem.gla.ac.uk/~louis/software/ortep3/)

GUI WinSTRUPLO (http://www.chem.gla.ac.uk/~louis/software/struplo/)


Slide 83

Photorealistic rendering of structuresGUI WinORTEP / GUI Struplo / WinGX

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

• Can open a wide variety of file formats including GSAS!


Slide 84

Ton Spek’s Platon Addsym - finding extra symmetry and exploring symmetry in simple to complex polymeric

inorganics

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

• One of the best programs for finding missing symmetry from crystal structure information.

• Now has enhanced subcell finding

• Now has enhanced defaults for inorganics


Slide 85

Ton Spek’s Platon Addsym - another spectacular example

• Triclinic Cell - P1– structure calculated

by an-initio methods

– (96 independent Carbon atoms)


Slide 86

Ton Spek’s Platon Addsym - spectacular exampleRun Platon’s Addsym in default mode

• Addsym finds the true cell - which is a 1/8th subcell– (3 independent

Carbon atoms)

– Monoclinic P 21/c

– (compared to 96 atoms in the starting structure)

– Can be just as effective for ab-initio calculations on minerals.


Slide 87

Platon’s Addsym - finding extra symmetry in hand- build inorganic models

• In the GSAS refined ceramic - original starting “model” was hand-built using crystal chemical arguments in R3

• Platon’s Addsym (default values) gives R-3c – plus option of a new Shelx RES file with the

structure in the new spacegroup– and the directions to find the extra symmetry

elements from the old R3 model


Slide 88

Platon’s Addsym - finding extra symmetry in powder refined structure in triclinic

• Model refined in C 1

• Platon’s Addsym can get back to R3 except one interstitial metal site seems to be breaking the symmetry and keeping the triclinic symmetry.

• Got to be careful how you use this :– e.g., increasing the values for the defaults can get

you back your “ideal” non-tilt model


Slide 89

Summary • Help show some of the potential of using GSAS and EXPGUI for

some of your mineralogical and inorganic powder samples.

• Show other programs that can be of assistance - Platon, WinGX, Jana, VCTCONV, Powder v 4, etc

• Many of the listed resources are available or mirrored at:

http://www.ccp14.ac.ukThanks:

– Bob von Dreele and Alan Larsen - GSAS Rietveld

– Brian Tony - EXPGUI

– Ton Spek - Platon

– Mark Bowden - Vctconv

– Louis Farrugia - WinGX

– Ian Grey, Gus Mumme, Bob Roth, et al - High-tech ceramic example

Documents

A structure is not truly solved until it is refined! : tricks and hints for using Alan Larson and Bob von Dreele's GSAS, and Brian Toby's EXPGUI, for combined