This tutorial focuses on the solving of an organic structure, for which only low-resolution single crystal data is available. Data courtesy of A. van der Lee (CNRS, Univ Montpellier, France). (the data was recorded on purpose at low resolution).
- single crystal data
- molecule formula
- unit cell (5.957,9.031, 18.384) and spacegroup (P212121), as determined from the single crystal diffractometer
All these are available in the directory "Fox/examples/tutorial-ylid".
Create the crystal structure
- After launching Fox, use the top "objects" menu to create a crystal structure.
Enter the unit cell (5.957,9.031, 18.384) and spacegroup (P212121)
To enter the molecule, we need a model. If you search using google for "YLID C11H10O2s"), you will quickly find the correct molecule: e.g. on chembase: from that page you can download the structure as a 'mol' or 'sdf' file. You can then convert it to a Fenske-Hall z-matrix which Fox can read, using openbabel: "babel ylid.mol ylid.fh". Alternatively, you can use the ylid.fhz file in the tutorial-ylid directory.
Then use the crystal menu "Scatterers->import Molecule from Fenske-Hall z-matrix". This will import the molecule, and automatically assign bond lengths and bond angle restraints.
Use the menu "Diplay->3D display" to open a 3D view of the crystal structure.
- You can give a name to your crystal, e.g. YLID
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".
Single crystal data
Use the top "objects" menu to create a new single crystal data object.
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.
- Note that the single crystal data automatically selected the YLID crystal, since it is the only crystal structure in memory.
Open the graph using the menu "Data->show graph". This will display a powder-pattern like graph, with the obs/calc values as a function of 2sin(theta)/lambda. it is useful to see the optimization progress.
Use the top "objects" menu to create a new Monte-carlo Object.
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.
This is a simple structure, so you can set the number of trials to 100000.
Set the option "Automatic least squares refinement" to "At the end of each run".
Save your project using the top menu "File->save". It will be written in an xml file (format specific for Fox), and compressed with gzip.
In the Global Optimization object, use the menu "Run/Stop->Multiple Runs".
- 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. 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.
Once a few runs have been made, you can use the menu "Run/Stop->Stop optimization". You should see that the fit in the graph of the single crystal data is reasonably good, and that the structure is reasonable, i.e. without any overlap between molecules.
Since you ran multiple runs, you can use the menu "Solutions->browse solutions", and every time you click on one, it will update the displayed structure and data. All structures should be identical (or symmetrical), except for the hydrogen positions which cannot be found with this low-resolution dataset.
You can Save your project using the top menu "File->save", to write it using Fox's xml format.
You can export you structure as a CIF file using the menu in the crystal object "File->save as CIF". You can also export it as a text file.
Finally, you can compare the structure with the one in the crystallography open database (COD).