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Tutorials and Examples

CRYSTALS Single Crystal Suite

Difference Fourier Map of an Organic Structure using Crystals

The CCP14 Homepage is at http://www.ccp14.ac.uk

[Tutorials page] | [Crystals Tutorial page]


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)

Opening an existing refinement


It is possible to use an \edit command to set the fractional occupancies of the Hydrogens to 0 (described in the Inorganic Fourier Map generation tutorial page). But as it is quite easy to automatically add the Hydrogens back in. We may as well delete the hydrogens using the Structure, Remove Hydrogens menu option.

Result of having removed the hydrogens


Now select atoms that will define the slant plan using the mouse. They should light up after being selected.

Crystals after selecting 3 atoms.


With the mouse cursor over one of the selected atoms, click on the right mouse button to bring up the various allowed options; including a Slant Plane Fourier Map option.

Going into the Slant Plane Fourier Map Option


The default option for Slant Plane fourier is Fobs. Select difference for a difference map. Normally, some trial and error can come into this. For this example, a 10 Angstrom section with 4 sections each side was found to give OK results. The result will then be viewed automatically in Michal Husak's MarchingCubes for Windows program. As a reminder, make sure you have selected Difference map as Fobs is the default. Just press OK to continue.

Slant Plane Fourier Map Options


You should then obtain something similar to the following map. If the maps looks like it is saturated with peaks, it could be that you actually calculated an Fobs map. If so, redo again. Also, if the "green" contour obscures things too much; just use the slide to optimise the contour levels for the 3 different available colours. By interacting with the 3D map using the mouse, you can get a feel what is going on in electron density (real space). For instance, the following shows what might be interpreted at the hydrogen positions for the relevant atoms by setting the green, blue red contour levels to 2, 3 and 4 respectively. (red atoms are Oxygen, Blue atoms are nitrogen, carbon atoms are grey)

Difference Fourier Map as Displayed in MarchingCubes for Windows


The following image is the difference map applied using the benzene atoms to define the slant plane. Notice the hydrogens off the benzene ring and the 3 blobs of electron density off terminal terminal (grey) carbon.

Difference Fourier Map as Displayed in MarchingCubes for Windows


[Tutorials page] | [Crystals Tutorial page]

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