Single Crystal Structure Solution
Files needed: glycine.hkl
Learning outcomes: How to solve single crystal data using charge flipping in Topas. Structure refinement is done in a separate tutorial.
1. Save the hkl linked above in your directory. This was recorded using Mo radiation and processed using Saint plus and xprep. These packages suggest the space group is P21/n and give cell parameters of a = 5.092, b = 11.819, c = 5.462 Angstroms, beta = 112.00 degrees.
2. Open a blank document in jEdit and save file as glycine_solve.inp.
3. Go to “Templates” in the Topas_Durham menus and select the template for charge flipping using single crystal data.
4. As with all templates you need to change the purple text after” ->” arrows to appropriate values for your data (and delete the arrows), i.e. remove all purple text! In this case the template has the correct values for glycine data in place so you can just delete the arrows “->”.
5. Send to topas and run. After a few cycles you can stop charge flipping and view results.
6. To find atomic coordinates, go to the structure viewer window and open the “temporary output” text box. Then open the cloud dialogue. Tick the “with symmetry” box then click on “pick”. Atomic coordinates in str format will appear in the text box.
7. You can use these a starting coordinates for a single crystal refinement in place of the .cif file in the structure refinement tutorial. If you do this you’ll have to find hydrogens using a difference Fourier map.