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Once a few runs have been made, you can use the menu ' Run/Stop->Stop optimization'. You can follow the evolution of the fit in the various windows, including the 'Tracked data' graph which shows the evolution of Chi^2 as a function of the number of trials.

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This is a very simple structure (there is only a single free torsion angle in the molecule, if you do not take hydrogens into account), so it will converge almost immediately.

In the Global Optimization object, use the menu 'Run/Stop->Multiple Runs'. It will be written in an xml file (format specific for Fox), and compressed with gzip. Save your project using the top menu ' File->save'. Set the option ' Automatic least squares refinement' to 'At the end of each run'. This is a simple structure, so you can set the number of trials to 100000.

In the Global Optimization object description, use the menu ' Optimized Object->Add object to optimize', and add both the crystal and the single crystal diffraction data objects. Use the top 'objects' menu to create a new Monte-carlo Object. it is useful to see the optimization progress. This will display a powder-pattern like graph, with the obs/calc values as a function of 2sin(theta)/lambda. Open the graph using the menu 'Data->show graph'.

Note that the single crystal data automatically selected the YLID crystal, since it is the only crystal structure in memory.

In the Single Crystal object, use the menu 'File->Import HKL Iobs Sigma' and select 'ylid1.hkl' from the tutorial-ylid directory.Enter 170 for the number of reflections. Use the top 'objects' menu to create a new single crystal data object. Since this is an organic structure, no atom is expected to fall on a special positions (though it can happen), so in the crystal structure description you can set the ' Dynamical Occupancy Correction' to 'No'.

You can give a name to your crystal, e.g.

Use the menu 'Diplay->3D display' to open a 3D view of the crystal structure. This will import the molecule, and automatically assign bond lengths and bond angle restraints.

Then use the crystal menu ' Scatterers->import Molecule from Fenske-Hall z-matrix'. Alternatively, you can use the ylid.fhz file in the tutorial-ylid directory. You can then convert it to a Fenske-Hall z-matrix which Fox can read, using openbabel: 'babel ylid.mol ylid.fh'.

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on chembase: from that page you can download the structure as a 'mol' or 'sdf' file. If you search using google for 'YLID C11H10O2s'), you will quickly find the correct molecule: e.g. After launching Fox, use the top 'objects' menu to create a crystal structure.Įnter the unit cell (5.957,9.031, 18.384) and spacegroup (P212121).unit cell (5.957,9.031, 18.384) and spacegroup (P212121), as determined from the single crystal diffractometerĪll these are available in the directory ' Fox/examples/tutorial-ylid'.(the data was recorded on purpose at low resolution). van der Lee (CNRS, Univ Montpellier, France).

This tutorial focuses on the solving of an organic structure, for which only low-resolution single crystal data is available.