Overview of 3D Crystal Structure Viewer

Overview of 3D Crystal Structure Viewer
In Jade 6, an external Java applet was provided to view the crystal structure in 3D. That applet is a small part of
MDI's jPowd program (a standalone powder XRD simulation application) and requires Java virtual machine to run.
Since Jade 7, that applet has been replaced by a brand-new 3D viewer, which is completely integrated into the XRD
simulation dialog (see the new 'V3D' tab), and does not rely on any external 3D graphics library (such as OpenGL or
Java) to run. This new viewer is loaded with rich features and now comes with the Jade Plus package since the XRD
simulation has been bundled into the licensed options of Jade Plus. Included are many features that may be especially
useful to those instructing students or those new to XRD. Among its notable features are:
•− True 3D ball and stick rendering of crystal structures with true colors, specular lighting, depth-shading, z-buffer
hidden surface removals and antialiasing for smoothed images.
•− Viewing options include wire-frame, outline, polyhedra, space-filling, stereo pair, anaglyph view, parallel and
perspective projections, multiple view ports and windows.
•− Real time rotation and zooming of large 3D views (up to thousands of atoms, bonds and polyhedra). You can delete
atoms in 3D view by point and click, and select atoms to calculate distances, bond angles, and torsion angles.
•− Visualization of translucent atoms, bonds, polyhedra, unit cell facets. A partial-occupied site, for example, can be
visualized by translucent atoms with their opacity linked to the occupancy factor. For cool-looking images, built-in and
custom textures can be rendered on atom surfaces, custom background image can be applied, and special effects
such halos, hulls and shades can be rendered around the atoms.
•− Visualization of translucent reflection planes, Bragg-cones and packing surface of 3D lattices from a list of possible
reflections. You can also compare packing surfaces of two different lattices from two crystal structures, and bring
them together in 3D by easy-to-use xyz-sliders and in-plane rotation tools.
•− Instantaneous re-simulation of complete powder diffraction pattern by dragging a symmetry-related atom in 3D
view.
•− Unique cavity search and visualization tools such as filling cavities with tiny 'ping-pong' balls, peeling and slicing of
a packed 3D volume along any viewing direction.
•− Comparison of two crystal structures in 3D (side by side or superimposed) with manual and automatic alignment of
3D orientations. A similarity index is also computed by Jade to gauge two similar structures.
•− Visualization of random atomic thermal vibrations (as indicated by the isotropic thermal parameters), and autotumbling
of 3D view by tug (this action will be described later).
•− Visualization of small organic molecules and large proteins with special rendering options and tools.
•− High resolution hardcopy printout, image file creation and built-in slide show for any list of crystal structures.
•− Export 3D view to POV-Ray (Persistence of Vision Raytracing program from 'www.povray.org').
Once you have loaded a crystal structure on the simulation dialog, you can view its atom list on the 'Atoms' tab and its
3D crystal structure on the 'V3D' tab.
3D Rendering Options - Vector Graphics vs Pixel Graphics:
There are two basic types of image rendering modes implemented in this 3D viewer:
•− Vector Graphics: 3D image is drawn with vector elements such as filled circles, line segments and filled polygons.
Colors are assigned to these vector elements rather than to individual pixels. Clipping of hidden surfaces are

accomplished by drawing the objects behind first (i.e. front objects are drawn last to cover the hidden surfaces). This
rendering mode is fast, consumes little memory, and is good for producing high resolution hardcopy printouts since
the image is readily scalable. The trade-offs are: (a) atoms look more like disks than spheres, (b) bonds are thin, (c)
no translucent view and reflection planes, (d) unit cell outline may not be properly clipped, (e) interpenetrating objects
can't be drawn correctly.
•− Pixel Graphics: 3D image is rendered pixel by pixel on screen, in which individual pixels on the surfaces of 3D
objects can be assigned different colors and their depth values (z-buffer) are calculated to eliminate hidden surfaces.
This makes it possible to render (a) good-looking spherical atoms with texture, specular light and shaded colors, (b)
large cylinder-like bonds, (c) translucent atoms, bonds, polyhedra, reflection planes, unit cell facets, (d) properlyclipped
interpenetrating objects such as those in space filling and surface packing models. Pixel graphics is slower
compared to vector graphics, consumes more memory, and requires true 32-bit color desktop. High resolution printout
of pixel graphics depends on the amount of your video memory because Jade can internally render 3D images that are
much larger than the screen size and then scale them directly to the printer page. Note: speed of pixel graphics is less
sensitive to structure size than image size (i.e. smaller image window speeds up pixel graphics).
You can switch image rendering mode either by right-clicking the icon on the toolbar or from the mode selection
menu, which can be brought up either by left-clicking the icon or by right-clicking in the left half of image window,
as shown below:
Viewing options above the menu divider (except for the 'Smooth Edges', i.e. antialiasing) use vector graphics, and
those below are available only if the 'Pixel Graphics' item is selected. The above image of Biotite structure is rendered
in pixel graphics, and its vector graphics with polyhedral view in stereo pairs will look like the following (frontal light
only):

Notice the disappearance of buttons and dropdown lists from the dialog window in the above image. This compact
configuration is accomplished with the button at the end of dialog tabs or by pressing the Ctrl+H keys. Tip: you can
toggle quite a few dialog windows into compact forms in Jade by pressing the Ctrl+H keys.
Regardless of image rendering mode, a crystal structure can be viewed in parallel or perspective projection. You can
alter the viewing distance or vanishing point of a perspective view by left/right-clicking at the icon, while holding
down the Ctrl key, on the toolbar located just above the image window:

Depth shading also enhances the perspective of a 3D view by darkening 3D objects and blending them into the
background as a linear function of viewing depth. You can choose from ten different levels of depth shading by
left/right-clicking the icon on this toolbar - giving rise to five levels of darkening and five levels of blending (i.e. fade
into the background). An example of level-10 blending of 3D image is given below:

Rotating, Scaling and Zooming of 3D View
You can rotate the view simply by dragging with the left mouse button in the image window and zoom in or out by
dragging up/down with the right mouse button on the right half of image window. If you right-drag on the left half of
image window, Jade rotates the view around the z-axis normal to the screen. You can rotate the view around x,y,z-
axes by left/right-clicking the buttons in predefined stepping angles, and hold the Ctrl-key down to change
the stepping angles. You can also zoom in or out by the scroll-wheel or by left/right-clicking the button located at
the lower-right corner of image window and keep it depressed for continuous actions. You can enlarge or shrink all
atoms in the view by left/right-clicking the button or a particular species of atoms by left/right-clicking the atom
legend while holding down the Ctrl key. Jade determines the initial size of an atom species to display according to its
valences and the radius lookup table which is stored in the 'jade9.rds' file. You can change the display color of an
atom species by clicking its legend in the upper-left corner of image window - the color dialog will appear. If you
enlarge the atoms until they interpenetrate in pixel graphics, you will have the space-filling view of a crystal structure,
for example,
Tip: you can resize all atoms to several preset radii by left-clicking the button while holding down the Ctrl, Shift or
Alt key. Here is another example of space-filling view of a small molecule (Vitamin-E):

You can start automatic rotation (i.e. tumbling) of a 3D view either by selecting the 'Tumble' item on the following
menu:
or by tug in the image window if the 'Inertia -> Tumbling' is checked on the above menu. 'Tugging' means to let go
the left mouse button quickly while dragging the view. The harder you tug, the faster the tumbling, and this may take
some practice. You can access the above menu with the icon on the toolbar or by right-clicking anywhere in the
right half of image window. You can speed up or slow down the tumbling by pressing the ± keys on the numeric
keypad. If the 'Auto-Fit Rotation' item is checked on the above menu, Jade automatically rescales the 3D view to fit in
the image window during drag-rotation and tumbling. To stop the tumbling, you simply click in the image window.
Jade also stops the tumbling when you select another tab on this dialog or when this dialog is deactivated (lost focus)
by you activating other modeless dialogs or the main window of Jade).
The following keyboard and mouse scroll-wheel operations are also implemented for rotating, scaling and zooming of

3D view when the image window has the keyboard focus:
•− Arrow keys: rotate the 3D view left or right or up or down in the image window.
•− Shift + Arrow keys: shift the 3D view left or right or up or down in the image window. You can also drag the 3D
view directly with the left mouse button while holding down the Shift key.
•− Mouse scroll-wheel or ± keys: zoom in/out the 3D view. With the scroll-wheel, you can hold down the Shift, Ctrl or
Alt key to speed up zoom, resize atoms and alter the perspective of 3D view.
•− Ctrl and ± keys or Ctrl+Depress left/right mouse button anywhere in image window: enlarge or shrink all atoms.
•− Alt and ± keys or Alt+Depress left/right mouse button anywhere in image window: alter the perspective of 3D view.
•− Ctrl+Alt and ± keys: alter viewing angle of stereo pair (from 2 to 10 degrees).
•− Spacebar: reset 3D view to fit in the image window.
•− Most of the toolbar icons have shortcut keys indicated in their tooltips by square brackets. For example, you can flip
through all image rendering options (pixel and vector graphics) by pressing the V key.
When you zoom into a large crystal structure, you can choose the 'Walk into View' option to simulate the effect of
walking into a 3D view, i.e. viewing the structure from inside out. Jade simply hides the front atoms from view
according to the zoom factor (or viewing distance to the center). In addition to manual rotation, you can orient the 3D
view along a particular crystallographic axis (uvw) or along the normal of a reflection plane (hkl) from the 'Orientation
[uvw]' sub-menu. For example, you can snap the 3D view along its a,b,c-axis or the diagonal of its unit cell simply by
pressing the A, B, C, D keys on the keyboard. Note: fractional values are accepted for the [uvw] or (hkl) if you choose
to enter them manually. Notice that Jade also compute and display the current viewing direction (i.e. screen normal)
in terms of [uvw] and (hkl) at the right end of icon-bar, for example,
Tip: you can avoid a wide drawing window in order to see the [uvw] and (hkl) values by right-clicking the icon or by
selecting the 'Reset Display... | Hide 3D-Range Icons' sub-menu.
Display Range, Volume and Center of 3D View
By default, only the contents of one unit cell of a crystal structure is shown. The 'Atoms' tab on this dialog contains
the unique set of atoms which are not related by crystal symmetries (that's why it is called the asymmetry unit). Jade
generates the rest of atoms in the unit cell from the asymmetry unit using the symmetry operators defined by the
space group of the crystal structure. Once the unit cell is filled, it can be freely extended (i.e. repeated or stacked up)
along its crystallographic a,b,c axis. You can do so using the range slider or the icons on the toolbar to
include more atoms around the unit cell. You can extend a 3D view along its a/b/c axis by increment of one unit cell if
you click the icons and also hold down the Ctrl key. You can also build up a 3D view simply by pressing one of
the 9 numeric keys (i.e. 1 = unit cell, 2 = 2x2x2 volume, etc.) if the image window has the keyboard focus, or by
pressing the keys to operate the range slider. Regardless of how you extend the viewing range and volume, a
maximum of 30,000 atoms are allowed in a 3D view. Notice that Jade will reset the display volume back to one unit
cell in the default orientation when you load a new crystal structure into this dialog, but you can preserve a particular
viewing range, scaling, and/or orientation by unchecking the desired item from the 'Reset Display...' sub-menu. These
options may come in handy when you have a list of similar crystal structures to browse.

Also by default, a 3D view is centered at the middle of a unit cell, i.e at (0.5, 0.5, 0.5) in fractional coordinates, but
you can move the display center to a particular atom or any other spot in the unit cell from the 'Center of 3D View'
sub-menu:
Notice that Jade always displays the unit cell outline around the chosen center and this may violate the crystal
symmetries imposed by the space group when the center is not at (0.5, 0.5, 0.5). Beside the usual rectangular (or
triclinic) enclosure box of 3D view, which is bounded by the a,b,c axes, you can also have a 'Spherical Enclosure' view
around the chosen center of display. In this spherical enclosure view, the range slider controls the radius of
display volume (from 3-13Å) and the icons are disabled. You may find this enclosure useful in examining the
near atomic coordination environment of a large structure. For example, you can use the 'Center Sliders' in spherical
enclosure to show just one bucky ball of a C60 structure (e.g. FIZ# 66729):

Tip: this bucky ball can also be singled out by selecting the 'Hide Sited Atoms | Molecules Only' menu item (to be
described below), and then selecting the 'Center of Gravity' as the display center. Tip: you can indicate the center of
display by right-clicking the icon.
Visualizing Crystal Structures in Stereo Pairs:
You can view a crystal structure in stereo pair by left-clicking the icon, and select stereo options by right-clicking
the same icon, as illustrated below:
The 3D illusion is accomplished by a pair of images separated by a small rotation angle for your left and right eyes.
You can specify this rotation angle (default to 6 degrees) by selecting the 'Stereo Angle...' menu item. The 'Red-Blue
Scope' option produces the so-called gray-scale anaglyph (remember those 3D images sent back by the Mars Rover),

which can be viewed using any red/blue-lense viewing device (note: the red-lense should cover your left-eye).
Visualize Interatomic Bonds and Polyhedra in 3D View
Interatomic bonds and polyhedra are useful to visualize near coordination of atoms in a crystal structure. These three
icons and the distance slider on the toolbar controls the search and connection of interatomic bonds.
Using the slider, you can set the maximum bond length from 1.5Å to 3.5Å (2.5Å is the default cutoff), but Jade makes
some exceptions for hydrogen and covalent-bonds. Also by default, Jade will not connect from cation to cation or from
anion to anion for non-elemental compounds regardless of distance cutoff, but you can override this rule either by
right-clicking the 2nd and 3rd bond icon or by changing the valence assignment on the atom list. The 3rd bond icon
toggles the highlight (by different color) of double-bonds (if any) and/or 'abnormal' bonds whose distances are
deemed too short by Jade according to the built-in atomic radius table. You can view and edit this built-in radius table
using the button on the 'Bond' tab of this dialog. Notice that this radius table is different from the one (in
'jade9.rds') used to display atoms in the 3D view.
In vector graphics, you can have 1/3/5-pixel stick bonds by left/right-clicking the icon, and in the wire-frame view,
Jade displays half & half bonds using the colors of bonding atoms, for example,

In pixel graphics, you can render better-looking bonds. For starter, you can left-click the icon to choose one of the
10 thickness levels of cylinder bonds or toggle between the maximum allowed and bonds off by right-clicking the
same icon. Notice that the maximum thickness allowed also depends upon the atom radii and the zoom level of 3D
view - i.e. the more you zoom in or the bigger the atoms, the thicker the bond sticks become, for example,
You can also choose mono-color or mixed-color bonds, and set their metallic shininess from the 'Bond Color Type' submenu.
The Marcasite cell will look like the following with the 'faded-color' bonds:

You can change the color of mono-color bonds on the control panel that can be brought up by the icon on the
toolbar:
and set the opacities of atoms and bonds if desired, using the translucent controls on this panel. Note: the definitions
and functions of these controls are given in their tooltips. The Marcasite structure will look like the following with
30%-translucent bonds:

You can hide the control panel by clicking at a blank spot on it or by clicking the icon once more or by clicking in
the image window. You can keep this control panel open by checking the 3rd box on the control panel.
A partially-occupied or disordered site in a crystal structure, as indicated by the occupancy factor of less than 1.0 on
the atom list, can be visualized as hollow disks with the icon in vector graphics, for example,
and in pixel graphics as hashed (striped) spheres,

or as translucent balls (i.e. opacity = √(occupancy)) if the 2nd box on the control panel is checked,
Tip: you can change the size of atom legends and phase id in the image window by the icon on the control panel
and hide them selectively from the 'Reset Display...' sub-menu.
You can ask Jade to detect and display coordination polyhedra using the icon on the toolbar. Jade currently displays
only tetrahedra and octahedra. It must be pointed out that the bond-length slider controls the search of possible
polyhedra in the current volume of 3D display, and the minimum bond length for a possible polyhedron is 1.25Å. The
more atoms you have in the view and the longer the bond-length cutoff, the more polyhedra could be found and
displayed. Jade will not display polyhedra which are too distorted to pass the built-in criteria of a decent polyhedron.
When intersecting polyhedra are present in the structure, Jade will display the one whose center atom has higher
electronegativity. Note: Jade will not consider H, O, F as center atoms in polyhedral search. An example of polyhedral

display in vector graphics is shown below:
Jade uses the color of center atoms to render the facets of polyhedra and automatically shrinks the vertex atoms of
polyhedra in vector graphics for sake of proper clipping. Notice that the facets light up when their normals are rotated
into the viewing direction (i.e. front). For a better view of polyhedron stacking in a large and complex structure, you
can hide the atoms from the view by left/right-clicking the icon once more:
If both tetrahedra and octahedra are present in the structure, you can also view just the tetrahedra or octahedra by
left-clicking the icon to cycle through the viewing options. If the polyhedra share their edges or facets, some back
facets may become visible or improperly clipped in vector graphics when perspective view is shown. You can get

around this limitation by reducing the perspective of the view or by using parallel view and rendering in pixel graphics.
When you view a large unit cell with lots of polyhedra such as in a zeolite structure, vector graphics is superior in
rendering speed if antialiasing is off (i.e. no edge-smoothing). An example of a zeolite structure view with more than
500 polyhedra is given below:
In pixel graphics, you can render translucent polyhedra using the opacity slider on the control panel described earlier,
for example,
Notice that Jade will not draw the bonds inside the polyhedra if the transparency is less then 30%. For added viewing
flexibility, Jade can render polyhedra around center atoms which are disordered, as long as the splits are less than 1Å
apart and not more than 32 folds. An example of polyhedral view with split sulphur atoms (6 folds) is shown below:

You can also show concave polyhedra in pixel graphics, using the first check box on the control panel or by rightclicking
the icon, for example,
Jade will render these center-fins in fused/faded-color from the three bonding atoms if you choose fused/faded-color
bond option, for example,

Specular Light, Atom Texture and Background
While you can adjust the brightness levels of atoms in pixel graphics by left-clicking at the icon, with the starting
level being a gray-scale print, you can bring up the hidden light-control panel by right-clicking at the same icon to
adjust the light-direction and assign atom texture, among other things:
All the controls on this panel have tooltips on them and you are encouraged to experiment and discover what you can
do with these controls. For example, you can simply click and drag in the atom preview area to set light-direction, and
if your cpu is fast enough, Jade updates the 3D view as you drag the light spot. Note: if you choose the default frontal
light, Jade bypasses most options on this control panel for sake of speedy-rendering of pixel graphics. Tip: you can
move the panel by dragging it if you hold down the Shift or Ctrl key.

The above image will look like the following with the default light-spot and the 'cloud-5' atom texture:
and with the 'inverted-light' and without the texture,
and with the level-4 'sand-stone' finish,

You can have five different levels of sand-stone finish (left/right-clicking at the button), and render it on atoms
only or atoms+bonds or bonds only with the button. Translucent hulls, halos and shades can be rendered around
the atoms, for example,
If the 'Eccentric' option is selected, halos and shades follow the spot-light around the atoms. Note: Jade does not
render eccentric halos or shades around translucent atoms. The 'Outline' option eliminates the halos or shades in the
overlapping regions of display. You can extend or shrink the halos and shades using the enclosure-slider on the
control panel as shown below:

You can remove halos or shades by selecting the same menu item once more (i.e. unchecking it).
For atom texture, you can have flat-mapping of selected texture image or wrap it spherically on atom surface in three
different ways (the button). You might want to choose the 'grid' or 'diamond' texture to see the differences of
these spherical wraps. Tip: flat-mapping is faster to render than wrapping-texture. You can also control how much the
texture can blend into the atom surface by left/right-clicking at the button, tile the texture image with the
button, and rotate the same texture image for different atom species in the structure with the button.
For the ultimate in customization of 3D view, you can add to the texture list (the button) by cutting out an image
swatch from any picture, inscribe your company name from the 'Miscellaneous... | Background Name' sub-menu,
include the XRD pattern plot in the main window from the 'Miscellaneous... | Background Trace' sub-menu, and post a
background image from the 'Miscellaneous.. | Background Image...' sub-menu, for example,

You can use a background image of any size, and if necessary, Jade will stretch it to fit the screen when you maximize
the image window. Tip: you can flip through all background images in the same folder by the newly-appeared
button in the image window, and you should find your favorite desktop pictures in the '\windows\web\wallpaper'
folder on Win-XP.
For the 'Background Name', Jade blends your 'Institution ID' into the background like a water-mark. You can change
its font-size using the icon and set its opacity using the translucent slider (also for cell-facets, etc) on the control
panel. For the 'Background Trace', whatever that's currently in the main zoom window will be redrawn in subduedcolors
in the image background. You can create the illusion of a 'Mirror Lake' with the background image to enhance
3D perspective from the 'Mirror-Lake' options on the 'Miscellaneous...' sub-menu. An example of 'Wavy Mirror-Lake'
illusion is shown below:

You should see the 'waves' moved slowly to the 'shoreline' as you rotate or zoom the 3D image. You can create similar
illusion with a gradient background, and adjust the 'lake-horizon' by left/right-clicking at the icon on the control
panel, as illustrated below:

You can remove the 'mirror-lake' effect by selecting the same menu item once more (i.e. unchecking it).
Display Reflection Planes and Packing Surfaces in 3D View
You can visualize reflection planes and their Bragg-cones in pixel graphics from the 'Reflection Plane' sub menu:
If there isn't a list of calculated reflections already on the 'Reflections' tab of this dialog, Jade automatically calculates
all possible reflections in the current structure and displays the list by the image window for selection. An example of
this viewing option is given below with the 'lightning-2' atom texture:
When you choose a reflection on the list, Jade displays its reflection plane through the center of 3D view. Notice that
Jade automatically calculates the angle between the last two reflection planes selected by you, and prints it to the
message area in the main toolbar as well as in the status bar. You can display a plane of arbitrary (hkl) by selecting
the 'My (hkl)...' sub-menu and save it (the 'Save It' sub-menu) so as to visualize two intersecting planes. Jade will

ender the saved plane in the color specified for Bragg-cones (see below), for example,
and compute the angle between the saved plane and the current one on the reflection list.
Like the reflection plane, Bragg-cones are an imaginary construct to depict the reflection geometry of the Bragg
equation (2d×Sin(θ)/λ). They are drawn in symmetric θ-angle to the plane on either side to indicate the incident and
diffracted X-ray beams. Therefore, when you look straight down the edge of these cones, the plane 'lights up' as if it
reflects the X-rays, and the stronger a reflection (i.e. its calculated I% value), the brighter the plane. You can resize
the Bragg-cones or make them disappear altogether using the Bragg-cone slider on the control panel.
You can display multiple parallel planes (up to 9) of a reflection in the view, separated by its d-spacing, for example,
It should be pointed out that a reflection plane may not always intersect a lattice of atoms in the structure depending
upon the chosen center of display. Nevertheless you can move the display center to a particular atom if necessary, on
the 'Center of 3D View' sub-menu, to accomplish the desired intersection. Notice that these parallel planes will not
light up in unison during rotation in a perspective view, and the depth-shading level set by the icon also alters how

much lights these planes will reflect. You can hide the display of reflection planes by selecting the '0-Plane' option on
the 'Reflection Plane' sub-menu. Tip: you can specify the (hkl) of a plane that does not appear on the reflection list by
selecting the 'My (hkl)...' menu item on the same sub-menu.
With the reflection plane in view, you can visualize the packing surface of atoms using the slicing options on the
'Reflection Slice' sub-menu, for example,
Jade would slice a layer of atoms out of the current display volume in the specified thickness starting from 0.5Å above
the reflection plane. Using the range controls described earlier, you can increase the display volume to extend the
packing surface, but you need to click at the reflection list again to cut out the extended slice.
You can click on an atom in the view to read its fractional coordinates, its distance to the center of display (R). Jade
will then calculate the distance of the last two atoms you click on, the bond angle of the last three and the torsion
angle of the last four. After you have selected an atom, you can delete it from the view, if desired, either by pressing
the Delete key or by right-clicking it again to bring up the atom-specific menu as shown below:

The ability to change the color of a specific atom in the display will come in handy when you want to highlight a
particular site on the packing surface. Tip: you can select multiple atoms for deletion or color change. You can remove
the highlight-circle of a selected atom by clicking at it again or clear all of them by clicking at the newly-appeared infolabel
in the image window or in the bottom info-bar.
Comparing Packing Surfaces of Two Structures:
Once you have obtained the desired packing surface of a reflection plane in a structure, you can save it for 3D overlay
with another structure by the icon on the toolbar. A new icon will appear, next to the icon on the toolbar, to
indicate the presence of a saved view and to let you clear it. You can then proceed to load another structure into the
3D viewer and cut out the desired surface to compare in the similar ways used to produce the saved view. When this
2nd surface is ready, you can click the icon again to overlay the saved view. Note: the saved view will be lost upon
closing this dialog. An example of comparing the (002) surface layer of graphite with the (111) surface of diamond is
given below:
This particular view is produced by the following steps:
•− Load the graphite structure and change the center of display to one of the carbon atoms on the atom list.
•− Generate the packing surface by extending the viewing range along the a & b-axes using the icons.
•− Change ID labels of carbon atoms to Nitrogen (N) on the atom list to show graphite layer in different color.
•− Select the (002) reflection, cut out the (002) plane in 3Å slice and save it by clicking at the icon.
•− Load the diamond structure and change the center to (0.0, 0.0, 0.0) on the 'Center of 3D View' sub-menu.
•− Extend the viewing volume of diamond lattice by dragging the range-slider half way to the right.
•− Select the (111) reflection, cut out the 3Å slice and click the icon again to overlay the graphite layer.
•− Separate the graphite layer from the diamond by dragging the newly-appeared z-slider upward.

If you look at these surfaces straight on, you should see the flat carbon rings in graphite vs those buckled in diamond.
Notice that Jade will automatically align the overlay in parallel to the current reflection plane regardless which plane
was selected in either structure. The newly-appeared x,y,z-sliders in the image window allow you to slide the overlay
along the current plane and separate it from the plane. The button will perform the in-plane rotation of the overlay
for additional docking freedom. If you want to compare the overlay to another plane in the reflection list of current
structure, you can click the button for auto-alignment or rotate the overlay manually by holding down the Ctrl key
while you drag in the image window. An example of comparing the Si (111) surface with the GaAs (111) surface is
given below to illustrate the slight mismatch of the two lattices in parallel view:
Comparing Two Similar Structures in 3D View
If you do not display the reflection plane and slice in 3D view, you can save a structure for 3D overlay using the same
icon and load a similar structure to compare by clicking the icon again. An example of comparing two structure
descriptions of Albite mineral is given below:

Jade uses only vector graphics in comparing two similar structures, and all pixel graphics functions and polyhedra are
ignored in this comparison mode. In mono-image view, Jade automatically turns on the wire-frame view as shown
above in order to superimpose them. If you choose stereo-pair view with the icon, you will have a few more
options to view the two structures by right-clicking the icon multiple times - i.e. superimpose or not, wire-frame or
not, same color or not while superimposed, for example,
Regardless which viewing option you choose, you can rotate them together or orient one relative to the other if you
hold down the Ctrl key while you drag in the image window. This alignment action will activate the calculation of a
similarity index to be displayed after the icons and in the message box on Jade's main toolbar. The
index is based on the average interatomic distances between the two structures within a 10Å sphere of display
volume. A similarity index of 100% indicates two identical structures. The icons let you adjust the cell
volume and dimensions of the saved structure if they differ significantly from the current structure. You may not see

some of these icons if the crystal system of the saved structure forbids the lattice constants to be changed.
Some similar structures are presented by very different choices of unit cells in terms of crystal symmetry (i.e. space
groups), cell origins and dimensions. For these crystal structures, manual alignment of two superimposed images will
be a challenge, and the auto-orientation icon may provide the rescue. For this auto-orientation to work, you must
choose one of the atoms to be at the center of display before you save the first structure. This atom should be the
one with a high degree of rotation symmetry such as the center atom of a polyhedron. When you click the icon,
Jade will automatically change the display center of current structure to the atoms of its asymmetry unit, and quickly
index through all possible orientations according to the rotation symmetry around the chosen center. If an orientation
with a similarity index greater than 65%, Jade will consider the two structures to be similar and display the orientation
of highest index in the image window. An example of auto-orientation of Amblygonite (FIZ# 48012) and Montebrasite
(FIZ#68926) structures is given below:
With a high similarity index of 98.9%, these two minerals are virtually identical even though Amblygonite is reported
by one author in 1959 as a P-1 cell and Montebrasite by another in 1995 as a C-1 cell. This auto-orientation is done by
choosing the first Al atom of Amblygonite to be the center of display and a spherical enclosure of about 90 atoms. If
you click at the 'Similarity Index' label on the icon toolbar, you can convert the atomic coordinates of saved structure
to the current setting.
Tip: you can also compare two similar or different structures by opening another 3D view dialog using the 'Compare'
button on this dialog. You can open as many of these dialog windows as you like, but not all 3D rendering functions
are supported on them.
Visualizing Cavities of Crystal Structures
In pixel graphics, you can visualize cavities and 'void' channels in large crystal structures such as zeolites from the 'Fill
Cavities with' sub-menu:

These options activate the search of cavities by Jade in the current display volume and fill them with the specified
'ping-pong' balls. The smaller the cavity balls, the finer details (i.e. resolution) of cavities will be revealed, but you
could generate too many of these balls to overflow the display limit. In this cavity search, the bond-length slider
controls the so-called 'buffer-zone', a surface layer wrapped around the packing of all atoms as defined by their atomic
radii (not display radii), which insulates the surface atoms from contacting the cavity balls. The thicker the surface
layer, the smaller the cavities to be filled with the balls. An example of cavity visualization of a zeolite structure is
shown below:
Notice the newly-appeared 'Cavity' legend in the image window and the strikeout legends to indicate hidden atoms.
Jade automatically hides the most popular atom species from the view after a cavity search, but you can choose which
atom species to hide by right-clicking at its atom legend. You can use the cavity legend like the regular atom legend to

change the display color and size of cavity balls. From the pop-up menu 'Peeling and Slicing', you can view the inner
cavities of a structure without hiding any atom by peeling or slicing layers of atoms from a filled 3D view. An example
of peeling the above zeolite structure along the diagonal of its unit cell is given below:
Visualizing Small Organic Molecules
While this 3D viewer was designed primarily to visualize inorganic crystal structures, a number of tools have been
implemented specifically for viewing small organic molecules and large proteins. Jade considers an input structure to
be organic if it contains carbon atoms among others and will make these tools accessible. The unit cell packing view
described above for inorganic crystal structures would produce molecule fragments in the unit cell due to symmetry
operations. Since a complete single molecule is often described by the asymmetry unit of atom list which may span
outside the unit cell box, you can view it by selecting the 'Asymmetry Unit' item from the 'Hide Sited Atoms' submenu:

Jade would disregard all symmetry operations and display the asymmetry unit as it. If the asymmetry unit describes
only part of a molecule or chelate, you can ask Jade to complete the display of the unique molecule or chelate by
selecting the 'Molecule(s) Only' item. An example of a small molecule view is given below:
Jade uses a built-in table of bond distances in molecule search. If this molecule or cluster spans more than one unit
cell or it connects and extends indefinitely like a polymer, you can set the limit for Jade to complete it using the 'Find
Molecule' slider located at the bottom of 3D control panel, which can be brought up by the icon:

Tip: you can replace the asymmetry unit by this newly completed molecule if you hold down the Ctrl key while
selecting the 'Asymmetry Unit' menu. You can label all atoms in the view with the icon and change the font size of
these labels by left/right-clicking the icon on the toolbar. If you right-click at the icon, you can label atom species
selectively from a popup menu, for example,
You can also identify an atom in the view by clicking on it directly - Jade will print its name and coordinates either on
the 'Info & Menu Bar' or in the image window if the info-bar is not shown. After you have selected one or more atoms
in the view, you can right-click in the image window to bring up the following menu:

The items above the divider on this popup menu apply to the selected atoms, and those below the divider apply to the
molecule of the LAST selected atom (therefore you only need to select one atom of a molecule for these operations).
The 'Center of View' item sets the center of rotation to the selected atom. The 'Count Elements' item generates the
chemical formula and molecular weight of the selected molecule or fragment. The 'Keep Just One' item removes all
other molecules except the selected one.
The 'Space Filling...' and 'Resize Molecule..' items let you specify the radius-multiplier of the selected atoms or
molecule or molecule fragment to render. An example of partial-packing view is shown below:

Tip: you can color or resize a fragment of a large molecule or chain by selecting two delimiting atoms, and then
choose the 'Color Molecule...' or 'Resize Molecule...' menu item. If you choose the packing model to view small
molecules in the unit cell or an extended range, you can ask Jade to trace and color all molecules or their fragments in
the current view from the 'Molecule & Protein' sub-menu:
and remove smaller fragments (defined by number of bonds/connections) from the 'Remove Fragments' sub-menu.
Notice that Jade uses random colors in the coloring operation and you don't have to color the fragments before
removing them. You can also color or remove molecules individually by clicking on an atom of a molecule or fragment
as described above.

If the asymmetry unit consists of a single molecule and you choose the 'Asymmetry Unit' display option described
earlier, you can see symmetry-related molecules in the unit cell from the 'Related Molecule(s)' sub-menu, which lists
the symmetry operators defined by the space group of crystal structure. Unlike the unit cell filling model, these
molecules will not be confined by unit cell box, for example,
In visualizing a complex structure, it may sometime be desirable to hide certain types or groups of atoms from the
view. Beside hiding a group of atoms related by symmetries on the atom list, as presented on the 'Hide Sited Atoms'
sub-menu, you can hide a species of atoms, such as all oxygens, simply by right-clicking at its legend - a red line will
strike over the legend to indicate the status as such, for example (hydrogens are hidden),

Notice that hiding a species of atoms does not affect its XRD powder pattern if you choose to simulate one, but hiding
a group of symmetry-related atoms on a symmetry site does. This is why a ? mark is shown in the 'Site' column of
atom list when a site is hidden. You can toggle this ? mark on or off by double-clicking at the 'Site' cell as well.
You can display translucent hulls around atoms to simulate space-filling or electron clouds, for example,
Tip: these atom hulls are best viewed on a bright background. The default radii of these spheres are set at 1.0x of
atomic radii, but you can enlarge them using a range-slider as illustrated above.

Visualizing Large Protein Molecules
Jade reads a few popular organic structure files such as Cambridge data file (*.dat, *.fdat), Protein Data Bank file
(*.pdb, *.ent) and *.mol file, and up to 30,000 atoms per structure model can be read from one of these files. If you
open such a file on this dialog or drag&drop it to the image window, Jade will turn the dialog into a 3D molecule
viewer-only form (i.e. other tabs on this dialog will not be accessible) since there is no space group or translation
symmetry to consider. In this case, the center of display is initialized to be at the molecular center of gravity, but you
can change it to any selected atom if desired. Tip: you can indicate the center of display by right-clicking the icon.
Double-bond info will be read from the *.mol file, if any, and displayed as such (but they won't follow the spot-light).
You can flip any single-bond to a double-bond (and vice versa) either by double-clicking at it directly or from the
popup menu after selecting the two bonding atoms. An example of a *.mol file display (caffeine molecule) is given
below:
You can find these sample *.mol files in the 'csd' folder of Jade. For protein structures, Jade provides a number of
specialized viewing options such as amino-acid color and highlight, backbone color and highlight, localized viewing
volume, and PIP zoom. An example of viewing a DNA segment is shown below:

This particular view is made by (a) selecting the 'Highlight Backbones' and then the 'Color All Molecules' items on the
'Molecule & Protein' sub-menu, (b) left-click at any one of the atoms in one strain and right-click to bring up the
selection menu and to select the 'Resize Molecule...' item, (c) repeat step (b) for the other strain, as illustrated below:
If the 'Highlight Backbones' is checked, Jade will color or resize only the backbone atoms when you choose to color or
resize a molecule. In addition, you can color or resize a selected groups of atoms or peptide segment in three different
ways:
•− Select the atom groups by clicking at the atoms one by one, and then right-click to select the 'Change Color...' or
'Space Filling...' menu items. Jade clears all selections if you redraw the image or you can clear them by clicking at the
status bar where the info of selected atom is displayed.
•− Select the peptide segment by clicking at two ending atoms, and then right-click to select the 'Color Molecule...' or

'Resize Molecule...' menu items. Jade will color or resize all the in-between atoms connected to the two ending atoms.
•− Bring up the atom list from the 'Miscellaneous... | List of Coordinates' menu, select the atom groups or peptide
segment from the list (drag or hold down Shift or Ctrl key), and then right-click to select the 'Change Color...' or
'Space Filling...' menu items. An example of this operation is given below:
You can focus your view to a small region of a large protein in three different ways:
•− PIP Zoom: you first check the 'PIP upon Atom-Click' on the 'Reset Display...' menu, and then click at any atom in
the 3D view to see the PIP zoom, for example,

•− Spherical Enclosure: you simply drag the range-slider to set the radius of enclosure-sphere around the current
center of display. Notice that Jade fades out the surrounding atoms in this view. If the 'PIP upon Atom-Click' is
unchecked, you can double-click at any atom to zoom around it. To revert to full-range view, you drag the rangeslider
to the left or simply right-click at the range-slider. An example of this view is given below:
Tip: you can also select an atom to be at the center of this view from the 'List of Coordinates' when the range slider is
set.

•− Amino/Nucleic-Acid Highlight: you first click at an acid atom and then right-click to select the 'Highlight Acid' menu
item (or press F3 key). Jade fades out the four adjacent acids in this view and you can change the highlight to them
by pressing the Ctrl+Arrows or left/right-clicking at the newly-appeared button in the image window. Press F3
again to revert to full view. An example of this view is given below:
If your *.pdb file contains multiple structure models, Jade will list them by the image window for you to select. You
can omit all hydrogens and water molecules in reading a large protein file in order to speed up the display.
Miscellaneous Features in 3D View
Dynamic XRD Simulation by Dragging Atoms in 3D View:
With ever more cpu power at your disposal, it would be a shame and a waste of that power if you can't alter a
calculated XRD powder pattern instantaneously by dragging an atom in the 3D view. With highly optimized simulation
engine built into Jade 9, you can do so on a decent 1GHz pc even with a complex structure yielding thousands of
reflections. Since atoms are related by symmetry operations in a crystal structure, it would be logical to present the
asymmetry unit as draggable atoms on the 'Atom (xyz) Sliders' sub-menu. When you choose one of these atoms to
drag, its xyz-sliders would appear in the image window if its x and/or y and/or z-coordinate are variable. You will see
all symmetry-related atoms moved at the same time in the 3D view as you drag the xyz-sliders. If an atom is located
at a special site such that its y and/or z-coordinate are linked to its x-coordinate, Jade will adjust the y and/or zcoordinate
accordingly when you drag the x-slider, so as to maintain its site symmetries.

Tip: you can reset a coordinate to its original or starting value by right-clicking at its slider, or make a backup copy of
the current structure by clicking the Compare button on this dialog.
If it takes less than 1/4 second to calculate an XRD powder pattern from the current structure, Jade will automatically
update the calculated pattern in the zoom window while moving the atoms by the xyz-sliders. Therefore you must first
click the Calc button on this dialog to let Jade determine the speed of simulation, and a depressed button above
the image window indicates a fast-enough cpu. If not, you may still overcome the 0.2 second threshold by limiting the
upper 2θ angle specified on the Calc tab. Notice that it's up to you on how to display the calculated pattern during
dynamic simulation - i.e. whether or not to generate profile trace on the reflection markers, or to label them with I%,
(hkl) etc. using the quick annotation toolbar, or to select a particular 2θ range in the zoom window.
Tip: you can also adjust atomic coordinates on the Atom tab and unit cell parameters on the Phase tab to perform
dynamic simulations. See the Calculate XRD Powder Pattern topic for more information.
Multiple Viewports, Ruler and Vectors in 3D View:
You can split the image window into multiple viewports (2 to 4) by left/right-clicking the icon, for example,

You can rotate and zoom in these views independently in the same ways used for a single view. The last viewport you
click on also receives the keyboard focus for all valid keyboard operations such as rotating, zooming and orienting.
Notice that you can drag the vertical divider in 3-viewports to change the viewport partition, and some features (e.g.
stereo-pair and picking atoms) are disabled in multiple viewports.
While you can measure interatomic distances and angles by clicking on atoms directly, you can overlay a persistent
ruler-crosshair in the image window with the icon for added measurement functions:
The ruler is in Å scale and the circle of dots are 5° apart. Notice that Jade will flip the display to parallel view for sake
of measurement if perspective view is on, and the cursor coordinates and angle to the display center are printed at
the end of icon toolbar (you may need to widen the image window to see them). Tip: you can indicate the center of
display by right-clicking the icon.

You can display translucent unit cell box rather than its outline by clicking at the icon once more, and overlay 3D
vectors originated from the center of display in pixel graphics, to indicate directions of certain properties, for example,
Like the orientation vectors, these three vectors are specified in crystallographic axes (uvw). If you check the box
before the slider of a vector, the values of uvw also specify the vector length in units of cell edges. When it is
unchecked, the uvw values specify only the vector direction and the slider sets its length from 1-10Å. Tip: you can set
the opacity of unit cell facets using a slider on the control panel.
Slide-Show of 3D Views from a List of Crystal Structures:
You can start a slide show of 3D views for a list of crystal structures from the 'Miscellaneous... | Begin Slide-Show'
sub-menu:

Refer to the Structure Database Manager topic for how to compile a list of structures and attach it to this dialog (as
shown above) using the button on that dialog. For each structure on the list, starting from the highlighted and
down, Jade will render its 3D image in the current graphics settings at real time, and randomly select one of half
dozen transition effect to introduce a new slide, and for which Jade also calculates and displays its powder pattern in
the zoom window. On a slow pc, you can reduce the size of image window to speed up the slide transition, You can
stop the slide show by clicking at the list or in the image window.
Like the slide-show, you can capture the 3D images to *.jpg files for each and every structures in the list starting from
the highlighted one, from the 'Miscellaneous... | Create Image Files...' sub-menu - Jade will prompt you to select the
destination folder to save the image files. You may find this output useful for thumbnail-browsing of structures in your
limited database. Tip: you can set JPEG image quality on the 'Misc' tab of user preferences dialog.
You can tabulate the coordinates of all atoms in the current view from the 'Miscellaneous... | List of Coordinates' submenu,
for example,

The x,y,z columns on the list are the fractional coordinates of atoms whereas the X,Y,Z's are their cartesian
coordinates (Å) in the current view. Jade will frame the atom in the image window (as shown above) when you select
it on the coordinate list. If desired, you can send the list to clipboard by pressing the Ctrl+C keys.
You can include the 3D image of a crystal structure in the printout of an observed or calculated powder pattern by
selecting the 'Miscellaneous... | Copy as PIP Zoom' sub-menu. Jade will send the current 3D view to the zoom window
as an image inset, which will then appear on the print preview window, for example,
Regardless of image rendering mode (i.e. vector graphics or pixel graphics), only bitmap image will be printed on the
hardcopy printout. You can remove this image inset by double-clicking at it. If you close this dialog but leave the PIP
window opened, Jade will update the 3D image with new structure when you select another phase on the main phase
list.

Saving, Copying and Printing of 3D Images:
The Print, Save, and Copy buttons on the simulation dialog apply to the 3D image when the V3D tab is selected.
Regardless of vector graphics or pixel graphics, the Save button always creates a *.jpg image file. The Print and Copy
buttons, however, produce a vector image in vector graphics vs a bitmap image in pixel graphics. You can capture
large 3D images (in multiple of screen sizes) in pixel graphics using the 'Print Quality' slider as illustrated below:
When you click at the Save or Copy button without holding down the Ctrl key, Jade captures what's shown in the
image window (image size = window size). If you hold down the Ctrl key with the Save or Copy button, Jade can
capture 3D images of much larger size depending upon the setting of 'Print Quality' slider, which sets the image size in
multiple of your screen size. The maximum size of 3D images that can be captured depends upon the amount of
virtual video memory your system has. Therefore high-quality 3D images of pixel graphics can be obtained on printout
when you send a large image (more pixels) to the printer with the specified print margins. For example, if you can set
the 'Print Quality' to 2x of screen size (say 1024x768), you can produce a >300 dpi image on a 6x4 inch printout.
Export to POV-Ray (Persistence of Vision Raytracer):
POV-Ray is a free ray-tracing program for rendering 3D scene and objects, which can produce stunning 3D images of
crystal structures with 'true' lighting conditions, and you can download from 'www.povray.org'. You can export most of
what you see in this 3D viewer to POV-Ray from the 'Miscellaneous | Export to POV-Ray...' sub-menu. Jade will then
write a 'user-id.pov' file using POV-Ray's scene description language in the Jade setting folder. If you have POV-Ray
installed on the pc, it will start with this file loaded, ready to be rendered by clicking the 'Run' button in POV-Ray. An
example of POV-Ray rendered image of crystal structure is given below:

A similar 3D image with the glassy look (a customizable POV-Ray parameter on export):
and a rutile unit cell with 25% reflectivity surface (another customizable POV-Ray parameter on export):

Note: an exported *.pov file is user-editable, but stereo pair of 3D images, background image and effects (such as
mirror-lake), image labels and legends are not exportable to POV-Ray. Tip: you can produce a stereo pair of POV-Ray
rendered images by exporting two separate 3D views in Jade - i.e. rotate the 2nd view by 6 degrees (pressing the left
or right arrow key 6 times).