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CrystalMaker makes it very easy for users to create
oriented surfaces - and there's a wide range of tools
available for doing this. In the following example, we'll
use the Lattice Plane tool to act as a guillotine, to
slice away atoms above and below the plane.
Once you've created your surface you may wish to place
molecules or other structures onto it. Note that since these
won't be consistent with the underlying,
crystallographic symmetry, you'll need to switch into
"molecule" mode, as described in step 11.
Instructions for creating an oriented surface:
Load your crystal structure into CrystalMaker
and ensure that your bonding and other display styles
are set up correctly. It's a good idea at this
stage to save a backup of your structure, in case
you need to return to it later.
Use the Transform > Set Range command to generate as
many unit cells as you need.
Choose the Transform > Lattice Plane > Show
command.
In the sheet/dialog that appears, enter the
orientation for your surface, set the
Show lattice plane option,
and click the OK
button to continue.
Your structure will now be replotted with a
translucent lattice plane slicing through the
centre.
Choose the Lattice Plane tool from the Tools
palette (if the Tools Palette isn't visible, you
can display it via the Window > Palettes > Tools
command).
Using the Lattice Plane tool, click and drag the
translucent plane so that it is at the correct position
for making a slice. Note that as you drag with the
mouse the plane moves along the direction of its
plane normal. You may wish to rotate the crystal to
get a better view.
(Tip: you can quickly rotate the crystal without
changing tools: hold down the space bar and you can
then rotate the crystal with the mouse; releasing
the spacebar brings you back into Lattice Plane
mode.)
When you're ready to slice your mode, choose the
following command: Transform > Slice Model.
- A sheet/dialog appears, prompting you to hide
atoms above or below the lattice plane. Click the
Hide Others or
Hide Selection buttons.
Your selected atoms (or unselected ones) are now
hidden.
Hide the lattice plane display by choosing:
Transform > Lattice Plane > Edit,
then unchecking the Show lattice
plane checkbox, and clicking the
OK button.
To define an oriented block of material,
use the Lattice Plane tool to move the lattice
plane slightly and then repeat steps 5-7.
To place a molecule onto your surface, you
will need to have the molecule saved as a
CrystalMaker binary "molecule" file (.cmmf).
Next, you'll need to discard your host (surface)
structure's crystallographic symmetry,
via the Transform >
Crystal to Molecule command.
You can then choose the File >
Place Molecule command to specify which
molecule should be placed into the current structure.
Finally, choose the Arrow tool from the
Tools palette, and drag your (selected) placed
molecule to where you'd like it positioned. (You
can also rotate this independently of the rest of
the structure, using the Tools palette's
Rotate Selection mode, which is detailed further
in the Online Help and full User's Guide.
Another method of creating a surface is to orientate
your crystal manually, e.g., via the
Set View Direction command, then flip it through 90° and
then use one of the Selection tools to isolate a block of
atoms.
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