[CCP14 Home: (Frames | No Frames)]
CCP14 Mirrors: [UK] | [CA] | [US] | [AU]

(This Webpage Page in No Frames Mode)

CCP14

Methods, Problems and Solutions

Powder Diffraction Structure Solution Pathways

Solving an Organic Structure (Cimetidine - C 10 H 16 N6 S) from Powder Diffraction Data

Le Bail fitting and generating an EXPO starting file using LHPM-Rietica

The CCP14 Homepage is at http://www.ccp14.ac.uk

[Back to: Problems and Solutions] | [Back to: Tutorials]
[Back to: Powder Diffraction Structure Solution Pathways Index]
[Back to: Solving an Organic Structure (Cimetidine) from Powder Diffraction Data]

[Back to: Initial Connectivity Searching of the Cambridge database for Cimetidine like molecules using CORINA, Platon and Quest/CSD]
[Back to: Peak Profiling of Cimetidine using XFIT]
[Back to: Powder Indexing and Spacegroup Assignment of Cimetidine using the Crysfire and Chekcell combination of programs]
[Back to: CELL Searching the Cambridge database via Platon and Quest]
[Back to: Le Bail fitting and generating an EXPO starting file using LHPM-Rietica]
[Back to: Solve the structure of Cimetidine using the Sireware EXPO direct methods software]
[Back to: Finding possibly missing Symmetry in cimetidine using the Platon ADDSYM option]
[Back to: Searching the Cambridge database via Platon and Quest for related strutures]
[Back to: Generating a 2D to 3D fragement for fragment searching using the web based CORINA; then getting into a Shelx format using Ortep-3]
[Back to: Solve the structure of Cimetidine using Sir97 Single Crystal Direct Methods Software]
[Back to: Solve the structure of Cimetidine using Dirdif fragment searching]
[Back to: Solve the structure of Cimetidine using ESPOIR with no restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with bond restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with a combination of rigid bodies freely moving atoms]

[To: Xfit-Koalariet Peak Profiling Software] | [To: Crysfire Powder Indexing Suite] | [To: Chekcell Powder Indexing Helper Tool] | [To: Platon/System S Crystallographic Toolset] | [To: LHPM-Rietica Rietveld for Win95/NT] | [To: EXPO Directory Methods Structure Solution from Powder Data] | [To: Sir97 Single Crystal Structure Solution Software] | [To: WinGX Single Crystal Suite] | [To: Espoir Monte Carlo Structure Solution Software]

This example uses example Cimetidine data from the EXPO software


A method to get Le Bail extracted HKL intensities is to use a variety of Rietveld packages. The advantage of this is you can have great control over the Le Bail fit - as well as model in secondary phases of a known structure. In this example, we will use the GUI LHPM-Rietica for Windows to do a Le Bail fit, output the extracted intensities in either Shelx or EXPO format, and generate an EXPO (*.EXP) control file.

For a full list of available programs that will do Le Bail fitting refer: Programs that will perform Le Bail extraction


Setting up the Rietica-LHPM input file

Assuming you have the data file already, start Rietica and select File, New Input.

Rietica New Input Window

Select under "Phases" that you wish to do an extraction and unless you already have the synchrotron diffractometer defined as an "instrument", stick to the defaults and we will change these in the input file later.

Tell Rietica we are doing an extraction

Select Model, General and setup the general information as shown in the following screen dump. Number of cycles, automatic Marquadt damping, data file format, we wish to obtain a EXTRA/Sirpow97 HKL file, and that we are using Synchrotron data.

Tell Rietica we are doing an extraction

This would be a good time to save and name the file. Select File, Save and browse to the directory that holds the Powder Diffraction data for cimetidine that you are using.

Select Model, Phases and input the basic information. That we want to do a Le Bail Extraction, Spacegroup and cell constants. the cell constants and two-theta offset should be from your unit-cell refinement so the Rietveld program should be right on the spot for starting the extraction. Le Bail fitting with an inaccurate cell can put you in a world of pain as the Le Bail fitting via the Rietveld software goes beserk.

Putting in cell, spacegroup information.

Select Model, Histograms and input the basic information. Setting the start, step and stop to zero tells LHPM to use the full pattern for the extraction. A Chebyshev function should be OK for fitting the background. Set the background function to refine.

Setting up the histogram information

Select Model, Sample and input the sample information. FJC Pseudo-Voight can be a flexible function to use that should work. As this is synchrotron data, set a thin width. Normally it would be good to fit a standard such as NIST/NBS Silicon or NIST/NBS Cerium Oxide to get good starting width and shape values. But if we don't have this information, starting off with a constant width should be OK.

Setting up the histogram information


Now we are ready to start the Le Bail fitting. The only parameters we are fitting at the moment are the background parameters. Select Rietveld, Refine, select the data file, select 10 cycles.

In the refinement area

Now start the refinement by selecting Start then Step. Don't be intimidated if the fit is very bad to start with. This is due to the initial eqipartition of starting intensities. Bad initial fits can also be due to problems width and shape. This will improve as we refine these options.

Starting the refinement

(be careful to watch for weirdess in the refinement. You will notice that in the following Rietveld plot, not all the HKLs are matching up with observered lines. This is because an error was made in the selection of the spacegroup (P 21/N instead of P 21/A). These errors are easy to make so always keep an eye out for errors of this sort. The screen dumps after this were made with the correct spacegroup.

zoomed area of tthe fit


Now go into a series of release parameter, refine set of refinement cycles. General (depending on the range of data and peak assymetry) releasing, i) zero offset, ii) unit cell, iii) W-width iv) gamma1 shape, v) V-width vi) gamma2 shape, vii) U-width, viii) gamma3 shape. (if necessary, the asymmetry (S/L and D/L) parameters can be released.) Depending on data quality, the parameters can be released in bunches or one at a time. You will only find out the hard way. Don't release the scale factor parameter as this is meaningless with Le Bail fitting.

Following is the fit after unitcell, 2-theta offset, V, W and Gamma 1 shape have been released.

Fit progressively getting better

Completed fit, all width and shape parameters, and one assymetry parameter.

Final fit


Completed Le Bail fit

The *.FOU file is ready for use in EXPO or processing by Overlap.

Using File, Export, you can create a starting Sirpow/EXPO file ready for structure solution. To use the following EXPO file created by LHPM-Rietica, all you have to do is name the FOU file, and put in the cell contents.

%window
%struct rietica
%init
%job Cimetidine                                                                  
%data
wavelength  1.52904
cell   10.3950   18.8207    6.8254   90.0000  106.4380   90.0000
space P 21/A              
ref2 xxxxxxx.fou - enter LeBail filename here
content  XX XX XX XX - enter expected cell contents here.
%normal
%continue


[Back to: Problems and Solutions] | [Back to: Tutorials]
[Back to: Powder Diffraction Structure Solution Pathways Index]
[Back to: Solving an Organic Structure (Cimetidine) from Powder Diffraction Data]

[Back to: Initial Connectivity Searching of the Cambridge database for Cimetidine like molecules using CORINA, Platon and Quest/CSD]
[Back to: Peak Profiling of Cimetidine using XFIT]
[Back to: Powder Indexing and Spacegroup Assignment of Cimetidine using the Crysfire and Chekcell combination of programs]
[Back to: CELL Searching the Cambridge database via Platon and Quest]
[Back to: Le Bail fitting and generating an EXPO starting file using LHPM-Rietica]
[Back to: Solve the structure of Cimetidine using the Sireware EXPO direct methods software]
[Back to: Finding possibly missing Symmetry in cimetidine using the Platon ADDSYM option]
[Back to: Searching the Cambridge database via Platon and Quest for related strutures]
[Back to: Generating a 2D to 3D fragement for fragment searching using the web based CORINA; then getting into a Shelx format using Ortep-3]
[Back to: Solve the structure of Cimetidine using Sir97 Single Crystal Direct Methods Software]
[Back to: Solve the structure of Cimetidine using Dirdif fragment searching]
[Back to: Solve the structure of Cimetidine using ESPOIR with no restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with bond restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with a combination of rigid bodies freely moving atoms]

[To: Xfit-Koalariet Peak Profiling Software] | [To: Crysfire Powder Indexing Suite] | [To: Chekcell Powder Indexing Helper Tool] | [To: Platon/System S Crystallographic Toolset] | [To: LHPM-Rietica Rietveld for Win95/NT] | [To: EXPO Directory Methods Structure Solution from Powder Data] | [To: Sir97 Single Crystal Structure Solution Software] | [To: WinGX Single Crystal Suite] | [To: Espoir Monte Carlo Structure Solution Software]

[CCP14 Home: (Frames | No Frames)]
CCP14 Mirrors: [UK] | [CA] | [US] | [AU]

(This Webpage Page in No Frames Mode)

If you have any queries or comments, please feel free to contact the CCP14