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