Note: the graphics manipulations through mouse functions on this page assume a 3-button-right mouse. For other settings of the mouse refer to "Mouse Functions" and make the necessary translations.
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If you have followed the instructions accurately, your 3D window should
now look very similar to the screen shot on the left. Obviously, only a
part of the whole molecule is rendered in the 3D window. Parts of the molecule
that lie outside the visible extent are "clipped". You may use the
command to increase the size of the visible extent in x&y by a factor of four. More conveniently, you may use the mouse to modify the display scale: with the left&middle buttons pressed, move the mouse up to increase the scale, move the mouse down to decrease the scale.Wit!P> display scale 0.25 |
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The display scale command only affected the visible extent in
the x&y directions. The molecule is still clipped in the z direction
(orthogonal to the screen). The distance between the near z-clipping plane
("hither"-plane) and far z-clipping plane ("yon"-plane) may be adjusted
with the mouse: with the Ctrl key of the keyboard and the
left&middle
buttons of the mouse pressed, move the mouse up, to move the "yon"-plane
away from the "hither"-plane, move the mouse down, to bring "yon" closer
to "hither". Alternatively you may set the distance between "hither" and
"yon" (the "slab width") by the
command.Wit!P> display set slabwith 7.5 |
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The screen shot on the left shows the effect of setting the slab width
to 7.5 Å. Note, that bonds in the back (near the "yon"-plane) are
drawn in faint, low intensity colors, to give an illusion of depth ("depth
cueing"). Since depth cueing is always correlated with the slab width (i.e.
max. color intensity at the "hither" plane, min. intensity at the "yon"
plane, the CLM (Ctr+left+middle) mouse function is frequently
used to adjust the amount of depth cueing.
Simultaneously press the Ctrl key and the middle&right mouse buttons, and move the mouse up and down: this will move the two z-clipping planes in concert (mouse up: move to back, mouse down: move to front). Or use the command to position the "hither" plane at 5 Å from the origin of the coordinate system.Wit!P> display set slabposition 5.0 |
On the next page, you will learn how to rotate and translate the molecule.