This tutorial continues on from Refining an Inorganic Structure using Crystals. Some of the thermals on the oxygens are quite large and worth investigating further. This is quite easily done in Crystals and a 3D Fourier map can be viewed in Michal Husak's MarchingCubes for Windows or the WinGX Mapview program.
The data used for this tutorial is:
If you exited crystRun Crystals, select File, New and go to the directory where the
previous refinement is located. (you can also browse
around via the Windows explorer and double click on the crfilev2.dsc file)
A new way of opening an existing refinement or quickly running Crystals in a desired directory is to run the Windows Explorer, go to the required directory and "right click" on the mouse. Then select "Open Crystals Here" to start Crystals in the required directory.
Click on the Anisotropic Thermals ICON to visualise the atoms anisotropically
Either click on an offending atom or select it from the bottom atom list. In this case, Oxygen 13, which has a large thermal value. Putting your mouse over the atom will tell you the atom label.
The trick here to get the difference map on the offending atom with the large
thermal is to give it a zero occupancy. Thus it will show up as the primary atom in the
The script method of doing this would be to use the following
If wanting to do this on more than one atom (e.g., O13 and O9), the command would have been.
Via the Graphical Interface, put the mouse over the offending atom and "right mouse click" and select the Edit menu and set the Occupancy to zero. If you wish to fix the parameters for this atom, put the mouse over the "Unselected" atom and "right mouse click" and go into the "Sticky refine mode".
Or you can go to the bottom right Atom List, put the mouse over the offending atom label and "right mouse click" and select the Edit menu and set the Occupancy to zero. Then Apply the Changes. If you wish to fix the parameters for this atom, put the mouse over the "Unselected" atom and "right mouse click" and go into the "Sticky refine mode".
Generating a slant plane Fourier map and viewing in Marching CubesMaking sure that WinGX is installed: Now select the O13, O11 and Si3 atoms by clicking on them. They should change colour after being selected. If you want the Map to be centred on the offending atom, put the mouse on this atom. Then right click on the mouse to bring up the Slant Plane Fourier Menu.
Then choose a Difference map and make sure the "Run 3D ELD Viewer" is selected. You may have to play around with the ranges of the slant plane Fourier map depending on the structure. Continue to generate the map and spawn Marching Cubes.
Then play with Marching Cubes to get the view you want. Arrow keys will give an offset. The "A" key zooms and the "Z" key resets.