Routine structure determination with SHELX: sucrose


This tutorial is intended to guide you step-by-step through a routine structure determination. It is intentionally very simplistic. In spite of what you may have been told, many structures are quite straightforward. You simply have to know what to do, which buttons to click, what to type, as well as when and how to make decisions. The structure in question is sucrose.


We pick up from the end of part 6 of the data reduction tutorial on this website. The last step there was to create a file with a '.hkl' suffix containing the scaled and merged dataset. To work through this example, you need two things - an '.hkl' file and the unit cell dimensions. From the kappaCCD diffractometer, the best estimates of the unit cell dimensions are in the file 'nreport.html', which is written by the program 'nreport'. The two files can be downloaded here:

sucrose.html
sucrose.hkl

This tutorial uses the still superb, but sadly now deprecated program, XP. Unfortunately, XP does not work so well on MacOS X versions after 10.4, unless you implement a straightforward workaround that installs an older version of the X11 windowing software. Do not worry, this workaround will preserve your official version of X11, as the two can co-exist side-by-side. In any event, XP works properly on Mac OS X after this fix, and it also still works perfectly well on linux and (so far as I know) on MS Windows.



Part 1: Setting up the instructions file - XPREP
Part 2: Structure solution - SHELXS
Part 3: Molecular editing - XP
Part 4: Structure refinement - SHELXL
Part 5: Thermal ellipsoid and packing plots - XP
Part 6: The Crystallographic Information File - CIF