Load input file for Structure Solution by Direct Methods
When default EXPO2014 fails: strategies
Suggestions
Contact and References
To run EXPO2014 for structure solution you need to create an input file (*.exp). You can create an input file accessing by graphic interface by the menu "File" > "New".
You must specify the structure name, the profile count filename and its format, the type of radiation source. It is supposed that the cell parameters and the space group have been determined before so fill the frame 'Cell Parameters' and 'Space Group'. Activate the check button 'Structure Solution' if you intend to perform the crystal structure solution process with Direct Methods. Otherwise use the button 'Open' to import an existing input exp, for example you could load the file cime.exp already existing in the directory 'examples'. The following picture is an example of the input file for crystal structure determination of the cimetidine compound.
When you press the button 'Save' an input file cime.exp will be created and automatically loaded by the program for the structure solution process by DM.
%structure cime filetype counts |
You can known the meaning of lines of the input file by looking at the chapter "command and their use" of this manual.
Alternatively you can edit a new input file or modify an exiting input file with a text editor and save it with extension '.exp'. Once a time the input file has been created, load the exp input file from menu 'File' > 'Load & Go'.
Press the button in the toolbar and the following steps of the structure solution process will be automatically performed:
1) Extraction of the integrated intensities from the powder diffraction pattern;
2) The integrated intensities are normalized via Wilson method (Wilson,1942);
3) Triplet invariants are calculated and their phases are estimated via P10 formula (Cascarano et al., 1984);
4) Phasing process: more plausible sets of phases are generated whose reliability is assessed via the CFOM figure of merit (Cascarano et al., 1992);
5) Twenty sets of phases with the largest CFOM values are stored and ranked in decreasing CFOM order. The first set of phases is automatically selected and used for computing an electron density map via an E-Fourier synthesis (E-map): the most intense peaks in the E-map are located and chemically interpreted. The obtained structure model is optimized and completed via the automatic structure model optimization.
More information about the structure solution process by Direct Methods are in the chapter 'The steps of structure solution procedure'.
A lot of crystal structures are solved by EXPO2014 by default settings in few minutes and in completely automatic way.
Unfortunately not always you can obtain the correct structure solution in default. In this situation two different strategies are suggested and can be applied at the end of the default run.
Explore trials
In a typical Direct Methods procedure more sets of phases (trials) are generated and ranked according to the combined CFOM figure of merit (estimating the quality of the trial) and only the best trial is used to calculate a Fourier map. Because of the unavoidable errors on the phases, the figure of merit can fail to evaluate the best trial, so it is strictly suggested to develop the other trials by menu 'Solve' > 'Explore trials'.
The following window will be opened (the procedure has been applied to 2-Mercaptobenzoic acid compound, whose input file is in the directory 'examples').
and the the CFOM value can be read. The highest CFOM value could not correspond to the correct solution while subsequent different trials may be successful. This is particularly true when several nearly equivalent CFOM's are available for different trials as in the picture. If the trial has been already developed (done='yes'), you can read the RF figure of merit value that quantifies the agreement between the structure factors extracted from the experimental pattern and calculated by the model.
Check the button in the first column to decide which trial will be developed and press the button If you check the button 'Select all new trials', all the trial not already explored will be automatically selected and developed.
You can choose three different actions for the structure model optimization (see later):
1)RBM: Resolution Bias Modification is the default action for organic and metal organic compounds.
2)Fourier: classical Fourier refinement, default choice for inorganic compounds.
3)E-map: the first electron density map calculated directly after the phasing process by Direct Methods.
4)COVMAP: the covariance principle based completion.
At the end of the procedure, all the trials will appear ordered according to the RF and the user can also view the model corresponding to each trial by mouse selection.
Alternatively to the graphical option, the use of the command %alltrials in the input file automatically activate the 'Explore trials' approach. An example of input file is here reported:
%Structure merca |
Structure model optimization
The structure model obtained at the end of the default strategy, generally is a partially correct representation of the true model: some atoms are in correct positions but other are incorrectly positioned or completely false. In this situation the user can try to improve the quality of the Fourier map, as obtained at the end of Direct Methods, by using different optimization strategies implemented in the EXPO2014 program:
It is possible to graphically choice different RBM procedures for model optimization by the menu 'Resolution Bias Modification (RBM)', via 'Refine' button from the upper EXPO2014 menu.
Apply the RAMM (RAndom Model based Method) procedure
The new method RAMM (Altomare et al., 2013) has been developed and implemented in the EXPO2014 computing program for improving the ab initio crystal structure solution process. When the available information consists of only the experimental powder diffraction pattern and the chemical formula of the compound under study, the structure solution classical approach follows two main steps: 1) phasing by Direct Methods (or by Patterson methods) in order to obtain a structure model (this last is usually uncompleted and/or approximate); 2) improving the model by structure optimization techniques. The alternative RAMM approach skips step 1) and supplies a fully random model to step 2). Such model is then submitted to important structure optimization tools present in EXPO: wLSQ , RBM and COVMAP which are able to lead to correct structure. RAMM is based on a cyclic process generating several random models which are then optimized. The process stops automatically when recognizes the correct structure.
Click 'RAMM' on the menu 'Solve' to activate this alternative strategy for structure solution at the end of the default run of EXPO2014. The following pictures are related to 2-Mercaptobenzoic acid whose input file is in the directory 'examples'.
The procedure can take from some minutes to several hours depending on the complexity of problem (number of atoms, quality of data, data resolution). If more than one plausibile solution is found they will be ordered according to the R-structure factor in an interactive list.
The selected model will be visualized on the molecular viewer. Press 'OK' to accept the selected model.
When Direct Methods procedure fails, the RAMM approach can be a very useful tool to find the correct solution.
The use of the command %randomsolve in the input file automatically activate the 'Explore trials' approach. An example of input file is here reported:
%Structure merca |
The number of options in the program is quite large. The optional strategies regard the improvement of both the decomposition process for carrying out more reliable reflection intensities and the Direct Methods performances. We give some other secondary strategies.
About the improvement of the decomposition process
About the optimization of Direct Methods procedure
For suggestions and bugs contact:
annagrazia.moliterni@ic.cnr.it
References |
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A.G.G., Rizzi, R. (2006.) Powder diffraction: the new
automatic least-squares Fourier recycling procedure in EXPO2005. J. Appl. Cryst. 39 (2006) 558-562.
Altomare, A., Cuocci, C., Giacovazzo, C., Kamel, G. S., Moliterni, A. & Rizzi, R. (2008a). Minimally
resolution biased electron-density maps. Acta Cryst. A64, 326-336.
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A. & Rizzi, R. (2008b). Correcting resolution bias in electron density maps of organic molecules derived by direct methods from powder data. J. Appl. Cryst. 41, 592-599.
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A., Rizzi, R. (2009) Correcting electron-density
resolution bias in reciprocal space. Acta Cryst. A65, 183-189.
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A., Rizzi, R. (2010a) The dual-space resolution bias
correction algorithm: applications to powder data. J. Appl. Cryst. 43, 798-804.
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A., Rizzi, R. The dual-space resolution bias
correction in EXPO2010. Z. Kristallogr. 225, 548-551.
A. Altomare, C. Cuocci, C. Giacovazzo, A. Moliterni and R. Rizzi (2012). Covariance and correlation estimation in electron-density maps. Acta Cryst. A68, 244-255.
A. Altomare, C. Cuocci, C. Giacovazzo, A. Moliterni and R. Rizzi (2013). RAMM: a new random-model-based method for solving ab initio crystal structure using the EXPO package. J. Appl. Cryst. 46,
Cascarano, G., Giacovazzo, Camalli, M., Spagna, R., Burla, M. C, Nunzi, A. & Polidori, G. (1984). The method of representations of structure seminvariants. The strengthening of triplet relationships. Acta Cryst. A40, 278-283.
Cascarano G., Giacovazzo C. & Guagliardi A. (1992). Improved figures of merit for direct methods. Acta Cryst. A48, 859-865.
Giacovazzo, C. (1998). Direct Phasing in Crystallography. Oxford: IUCr/Oxford University Press.
Wilson, A. J. C. (1942). Determination of Absolute from Relative X-Ray Intensity Data. Nature, Load.
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