Cerius2 Modeling Environment

9       Enhancing Model Display

The Cerius²·Visualizer includes many facilities for enhancing the display of your model, enabling you to interpret it better and to prepare effective graphical output.

This section explains

This section contains information on:

Model display colors

Customizing display colors

Surfaces--style and transparency

Lighting control

Rendering and ray-tracing

Stereo viewing

Important

Table 8. Finding information about enhancing model display

If you want to know about:	Read:
Changing color of selected atoms.	Coloring selected objects.
Changing color of all atoms of an element.	Default element colors.
Coloring atoms according to other characteristics.	Coloring atoms by properties.
Mapping atomic properties to colors.	Property-color mapping.
Changing the background color.	Background color in model window.
Changes colors used by the Cerius2 interface.	Interface colors.
Illuminating models from defined directions.	Directional lights.
Spotlighting parts of models.	Spotlights.
Labeling and annotating models.	Labeling and annotating models.
Changing the display resolution.	Resolution and graphical quality.
Printing models.	Printing models and graphs.
Exporting to non-Cerius2 applications.	Copying models to and from other applications.
Saving preferences.	Using saved sessions as preferences settings.

You should already know...

The basics of starting Cerius² and using its interface are demonstrated in Introducing Cerius2 and described in The Cerius2 Interface.

You need to know how to build (Basic building) and/or load (Loading model structure files) models. You should know how to select atoms in model(s) (Selecting atoms and groups of atoms) and how to position models on the screen (Moving models on the screen).

If your session contains several models, you should know how to specify the current model (Specifying the current model) or select atoms in more than one model simultaneously (Selecting atoms in several models).

Model display colors

Finding information

This section includes information on:

Default element colors

Coloring selected objects

Coloring atoms by properties

Background color in model window

Related information

Displaying labels and other information about atoms in a model is presented under Labels.

Saving nondefault settings for later use is described under Working with Cerius2 sessions.

Default element colors

Accessing the tools

Select the Build/Element Defaults... menu item from the main Visualizer control panel to access the Edit Elements control panel. If desired, access the Periodic Table window by clicking the periodic table tool in the upper right of this control panel.

Changing element default colors

Enter the desired element in the Current Element entry box, either by typing it in or by choosing it from the Periodic Table window.

Choose the desired color from the Display Color popup in the Edit Elements control panel. This is now the new default color for that element for the remainder of your current Cerius² session or until you change it again.

Example

A tutorial example of using the Edit Elements control panel to change default element colors is found under Changing atom colors.

Additional information

Please see the on-screen help for details on the functioning of each control in the Edit Elements control panel.

Coloring selected objects

Predefined "pen" colors

To color selected atom(s) or other object(s) with a predefined color, you can:

• Select the View/Colors... menu item to access the Color Selected Objects control panel, then choose a color from the Pen popup. (You can also access this control panel from the More Colors... pushbutton on the Annotation control panel, next paragraph.)

or:

• Select the Build/Annotation... menu item to access the Annotation control panel, then choose a color from the colors popup (to the right of the Line tool).

Mixing your own colors

To mix your own colors for selected atom(s) or other object(s), select the View/Colors... menu item to access the Color Selected Objects control panel.

Use the red, green, and blue sliders (or the entry boxes below them) to set the proportions of red, green, and blue in the final color.

Choosing colors from a color range

To choose colors for selected atom(s) or other object(s) from a range of colors, select the View/Colors... menu item to access the Color Selected Objects control panel. Click the Color Ranges... pushbutton to access the Color by Range control panel.

Choose any range from the list and check the Show Color Range check box if you want to display the color range (with color numbers) in the model display window.

Then enter the number of the desired color in the Use color number entry box.

You can edit color ranges to change them or create additional color ranges (see Color ranges).

Reverting to default colors

To set selected atom(s) or object(s) back to their default colors, select the View/Colors... menu item to access the Color Selected Objects control panel.

Set the Pen popup to DEFAULT.

Tip

Additional information

Please see the on-screen help for details on the functioning of each control in the Color Selected Objects control panel.

Coloring atoms by properties

Accessing the tools

Select the View/Colors... menu item on the main Visualizer control panel to access the Color Selected Objects control panel. This control panel can also be accessed by selecting the Build/Annotation... menu item and then clicking the More Colors... pushbutton in the Annotation control panel.

Coloring atoms according to a property

To color atoms according to a property, simply select them and choose the desired property from the Color by a Property list in the Color Selected Objects control panel.

You can create your own color maps for additional properties (see Property-color mapping).

Coloring a model according to multiple maps

To color selected atoms according to a cascading series of property color maps, click the Multiple Mappings... pushbutton in the Color Selected Objects control panel to access the Multiple Color Mappings control panel.

Use the arrows in this control panel to move selected maps between the Available Mappings and Selected Mappings lists and to change the priority of map application within the Selected Mappings list. Then click the APPLY pushbutton.

Any atoms that are not colored by the first map in the list (because they do not have the relevant property or because "as-is" coloring is specified for the relevant map value, Creating and editing a binary property color map) are colored according to the second map in the list, and so on in sequence down the list.

Returning to default atom coloring scheme

To return selected atoms to their default element colors, click the Reset selected object colors to default action button in the Color Selected Objects control panel. You also can set the Pen popup to DEFAULT (or click this popup if it is already set to DEFAULT).

Example

A tutorial example of using the Color Selected Objects control panel to color atoms according to a property is found in Coloring atoms according to a property.

Additional information

Please see the on-screen help for details on the functioning of each control in the Color Selected Objects control panel.

Background color in model window

Accessing the tools

To change the color of the model window background from the default black to something else, select the Utilities/Customize/Pen Colors... menu item to access the Pen Colors control panel.

Changing the background color

To change the background to white, black, or one of two shades of grey, choose the desired color from the Background popup.

To change the background to any color, either set the Pen popup to BACKGROUND or set the Background popup to OTHER. Then use the red, green, and blue sliders (or the entry boxes below them) to set the proportions of red, green, and blue desired in the background color.

Tip

Additional information

Please see the on-screen help for details on the functioning of each control in the Pen Colors control panel.

Customizing display colors

Finding information

This section includes information on:

Drawing colors

Color ranges

Property-color mapping

Accessing the tools

Select the Utilities/Customize/Pen Colors... menu item on the main Visualizer control panel to access the Pen Colors control panel.

Examining the currently defined colors

To display a window showing all currently defined standard colors, click the Show Current Pens action button. A Cerius2 Graphs window appears, showing all 16 pen colors.

Alternatively, you can show the pen colors as a color range within the model window by checking the Show Color Range check box in any control panel in which it appears (e.g., Property-color mapping) and selecting PEN_COLORS as the range to display.

The appropriate color changes when you redefine a color (next paragraph).

Changing the standard colors

To change one of the predefined colors, choose its name from the Pen popup in the Pen Colors control panel and use the red, green, and blue sliders (or the entry boxes below them) to set the proportions of red, green, and blue in the final color. (You cannot, however, change the name used for that color.)

Returning to the preset default colors

To return a single pen color to its default value, choose its name from the Pen popup and click the Reset Pen to Default action button.

To return all pen colors to their defaults, click the Reset all to Default action button.

Tip

Additional information

Please see the on-screen help for details on the functioning of each control in the Pen Colors control panel.

Color ranges

Uses of color ranges

Customized color ranges are useful for tasks such as:

• Highlighting an important point on a graph.

• Using a colored contour line within a greyscale diffraction pattern to highlight an interesting point.

• Appropriately changing all the colors used in a model to improve its visibility after the background color of the model window is changed.

• Changing a greyscale plot to a monochromatic colored plot.

Table 9. Some color ranges supplied in Cerius² and their typical uses

Color range	Some uses
pen colors	Structure displays in model window; simple line graphs; filled-circle plots.
color wheel	Mass cloud plots (Sorption module); probe surfaces for field calculations.
greyscale	HRTEM simulations; diffraction patterns, graphs.
electrostatic	Graphs (difference colors).
spectrum	Graphs ("color" colors).

Finding information

This section includes information on:

Creating and editing a new color range

Editing a color range

Concepts

To facilitate editing color ranges or constructing your own color ranges, several concepts need to be defined:

• Critical entries are points within a color range for which relative red, green, and blue color values are specifically defined and between which Cerius² automatically interpolates colors.

Each color range must contain at least two critical entries, defining the ends of the range (for example, only the two end values of the greyscale color range are defined).

A color range may contain more than two critical entries (the two endpoints and one or more points in between), as well as interpolated colors (for example, the electrostatic, color wheel, and spectrum color ranges have many critical entries).

A color range may be composed of only critical entries (for example, the pen colors color range).

• Noncritical entries are the automatically interpolated colors that lie between critical entries.

• The number of entries means the number of noncritical entries. The greater the number of entries, the smoother the color interpolation in the color range.

Viewing color ranges

You can display a color range in the model window by selecting the Utilities/Customize/Color Ranges... menu item from the main Visualizer control panel to access the Edit Color Ranges control panel. Then choose a color range from the Color Range popup and check the Show Color Range check box.

Identifying critical and noncritical entries

The numbers of the critical entries are displayed alongside the critical entries in the displayed range, facilitating their identification.

The numbers of the critical entries are displayed in a list box under Edit Critical Color Entries in the Edit Color Ranges control panel (whether or not you display a color range).

Selecting colors from ranges

To apply a color from a range to an object in the model window, see Choosing colors from a color range. (You can select a color from a color range by specifying the number of the entry (whether critical or noncritical) that corresponds to the position of the color in the range.)

Creating and editing a new color range

Select the Utilities/Customize/Color Ranges... menu item from the main Visualizer control panel to access the Edit Color Ranges control panel. Alternatively, if you have the Color Selected Objects control panel open (Accessing the tools), you can click its Color Ranges... pushbutton to access the Color by Range control panel and then click the Edit Ranges... pushbutton to access the Edit Color Ranges control panel.

Naming the color range

Type a name in the New entry box. Enter it by pressing <Enter> on the keyboard or clicking elsewhere in the control panel. Default values appear for the number of colors in the range and the numbers of the critical entries.

Defining the color range

Choose the number of color entries from the Number of colors in range pulldown. More numbers give you smoother color gradations, but you shouldn't set the number so high that it's beyond of your computer's graphics capability.

Set the colors of the critical entries at either end of the range by using the red, green, and blue sliders (or the entry boxes below them) to set the proportions of red, green, and blue in the color.

Tip

Add an additional critical color, if desired, by entering its position in the entry box for Add a new critical color and then defining the color by using the sliders. If you subsequently decide to increase the number of entries in the range, critical colors in the interior of the range maintain their approximate relative positions (for example, a critical entry at position 7 in a 16-color range becomes position 14 if you increase the number of entries to 32).

To change the position of a critical color (other than one of the end colors), enter a new position number in the entry box for Move selected critical color.

Saving a color range

You can save a custom color range by saving the current Cerius² session (see Saving the current session).

Additional information

Please see the on-screen help for details on the functioning of each control in the Edit Color Ranges control panel.

Editing a color range

Caution

Accessing the tools

Select the Utilities/Customize/Color Ranges... menu item from the main Visualizer control panel to access the Edit Color Ranges control panel. Alternatively, if you have the Color Selected Objects control panel open (Accessing the tools), you can click its Color Ranges... pushbutton to access the Color by Range control panel and then click the Edit Ranges... pushbutton to access the Edit Color Ranges control panel.

Selecting the color range

Choose the name of the range you want to edit from the Color Range popup. The current values for the number of colors in the range and the numbers of the critical entries appear. The color definitions appear in the sliders when you choose a critical entry from the Edit Critical Color Entries list.

If you saved the custom color range during some earlier Cerius² session (Saving a color range), you have to load that session to access that color range (see Loading a previously saved session).

Editing the color range

Edit the color entries by the same procedure as used in creating a color range (Creating and editing a new color range).

You can also use the Edit Color Ranges control panel to delete or rename an entire color range or to remove a selected critical color. (You should not delete either of the end colors.)

Additional information

Please see the on-screen help for details on the functioning of each control in the Edit Color Ranges control panel.

Property-color mapping

Uses of color maps

Customized color maps are useful for tasks such as:

• Coloring atoms according to their size or mass.

• Highlighting the backbone atoms of a polymeric model.

• Coloring atoms according to their isotropic temperature factors.

This section includes information on:

Creating and editing a binary property color map

Creating and editing a continuous property color map

Editing a property color map

Related information

Labeling atoms according to various properties is discussed under Labels.

You should already know...

Color mapping makes use of color ranges, so you should have some familiarity with them (Color ranges). In addition, you may want to define custom color ranges to use in your maps (Creating and editing a new color range).

Tip

Creating and editing a binary property color map

Select the Utilities/Customize/Color Mappings... menu item from the main Visualizer control panel to access the Edit Color Mappings control panel. Alternatively, if you have the Color Selected Objects control panel open (Accessing the tools), you can click its Edit Mappings... pushbutton to access the Edit Color Mappings control panel.

Naming your color map

Type a name in the New Map entry box. Enter it by pressing <Enter> on the keyboard or clicking elsewhere in the control panel.

What type of property is to be mapped?

Identify what type of property is to be mapped, by choosing an item from the Attribute popup in the Edit Color Mappings control panel.

Specify that the property to be mapped will use just two (on/off) colors, by setting the Type popup to BINARY.

The contents of the bottom of the Edit Color Mappings control panel depend on the value of the Type popup.

Setting the "on" and "off" colors

Set the color popups to the desired colors for the "on" and "off" values. You can also choose to color only the "on" or "off" value by setting the other to Use As-is.

To apply the map to your model, select the desired atoms and choose your new map's name in the Color by a Property list in the Color Selected Objects control panel (Coloring atoms according to a property).

If the map is already applied to your model, any changes you make to the on and off colors appears immediately in the displayed model.

More colors

If you want some color that's not available in the popups, click the More On Colors... or More Off Colors... pushbutton to access the On Color Selection or Off Color Selection control panels, respectively.

In addition to controls that are also available in the Edit Color Mappings control panel, these control panels allow you to:

• Define a custom color by using the red, green, and blue sliders (or the entry boxes below them) to set the proportions of red, green, and blue in the color.

• Select any color entry number from any already-defined color range.

You can save a custom color map by saving the current Cerius² session (see Saving the current session).

Additional information

Please see the on-screen help for details on the functioning of each control in the control panels mentioned in this section.

Creating and editing a continuous property color map

Select the Utilities/Customize/Color Mappings... menu item from the main Visualizer control panel to access the Edit Color Mappings control panel. Alternatively, if you have the Color Selected Objects control panel open (Accessing the tools), you can click its Edit Mappings... pushbutton to access the Edit Color Mappings control panel.

Naming your color map

Type a name in the New Map entry box. Enter it by pressing <Enter> on the keyboard or clicking elsewhere in the control panel.

What type of property is to be mapped?

Identify what type of property is to be mapped, by choosing an item from the Attribute popup in the Edit Color Mappings control panel.

Specify that the property to be mapped will use a color range, by setting the Type popup to CONTINUOUS.

The contents of the bottom of the Edit Color Mappings control panel depend on the value of the Type popup.

Setting the range of property values

Set the Minimum and Maximum Attribute Values between which the color map's range is to extend.

Tip

Coloring the values within the range

Decide what part of what color range to apply to the range of mapped property values by choosing the range's name from the Use Range popup and entering the Minimum and Maximum range-color entry numbers (in the Color Scheme section of the control panel). If you want to use the color range in reverse order, make the "maximum" smaller than the "minimum".

More colors

If you want, for example, to create a ternary mapping scheme rather than a full-color range or to highlight the outliers but not the intermediate values, click the More Colors... pushbutton to access the Range Mapping Color Selection control panel. In addition to controls that are also in the Color Scheme section of the Edit Color Mappings control panel, the Range Mapping Color Selection control panel allows you to:

• Set the intermediate values (i.e., those that are not outliers) to a constant color (with the Use Pen or Use RGB Color controls).

• Not apply any color to the intermediate values (Use As-is control).

Use the Outlier... buttons to access Outlier Handling control panels that govern how values beyond the minimum and maximum values are displayed.

You can handle outliers in any of several ways:

• Set outliers to a constant color (with the Pin to, Use Pen, or Use RGB Color controls).

• Set outliers to a constant color chosen from the same or a different color range (Use Color Range and Use entry number controls).

• Continue the color range beyond the maximum or minimum values (Wraparound control--the color range continues beyond the outlier, in head-to-head order, i.e., the order of the colors is not reversed).

• Do not apply any color to outliers (Use As-is control).

You can save a custom color map by saving the current Cerius² session (see Saving the current session).

Example

A tutorial example of using the Edit Color Mappings control panel to create a color map of atomic mass is found in Coloring atoms according to a property.

Additional information

Please see the on-screen help for details on the functioning of each control in the control panels mentioned in this section.

Editing a property color map

Select the Utilities/Customize/Color Mappings... menu item from the main Visualizer control panel to access the Edit Color Mappings control panel. Alternatively, if you have the Color Selected Objects control panel open (Accessing the tools), you can click its Edit Mappings... pushbutton to access the Edit Color Mappings control panel.

Selecting the color map

Choose the name of the map you want to edit from the Mapping popup. Its current defining parameters appear in the control panel.

If you saved a custom color map during some earlier Cerius² session (Saving a color map), you have to load that session to access that color map (see Loading a previously saved session).

Editing the color map

Edit the map definitions by the same procedure as used in creating a color map (Property-color mapping).

You can also use the Edit Color Mappings control panel to delete or rename a color map.

Additional information

Please see the on-screen help for details on the functioning of each control in the Edit Color Mappings control panel.

Surfaces--style and transparency

You should already know...

How to create surfaces is found in the documentation for the relevant application modules.

Accessing the tools

To set the style with which surfaces are made transparent, select the View/Display Attributes... menu item to access the Display Attributes control panel.

Setting the transparency style

Cerius² provides two methods for applying transparency to surfaces.

Set the Transparency Method popup to PATTERN or BLEND.

Blend transparency can be compared to looking at the model through a surface made of fine silk cloth.

Pattern transparency gives a screened effect, where the overall transparency is an average of a net of opaque and transparent areas on the surface.

Additional information

Please see the on-screen help for details on the functioning of each control in the Display Attributes control panel.

Lighting control

Important

If you prefer to learn by doing, you can skip the following discussion of concepts and proceed to Accessing the tools.

Finding information

This section includes information on:

Adjusting global light settings

Defining discrete light sources

Related information

Setting the graphical quality and screen resolution is discussed under Resolution and graphical quality. The screen coordinate axes are shown in Figure 3.

Concepts

An understanding of the following concepts can help you use the lighting controls effectively:

• The global ambient light (as controlled directly on the Lighting control panel) is general lighting in the scene that does not appear to come from any particular source.

• The ambient light component of defined lights is light that is scattered so much, by reflection from the "walls" enclosing the virtual scene and from objects within the scene, that there is no way to determine its original direction. Ambient light tends to take on the primary color of the surroundings and is most apparent in parts of the object that do not receive direct illumination.

• Diffuse light is scattered from an object in all directions; specular light appears as highlights on spherical or cylindrical objects. Matte surfaces are simulated by a high proportion of diffuse scattering; shiny surfaces by a high proportion of specular reflections. Diffuse light takes on (and in essence, defines) the perceived color of the object; specular light is usually the same color as the light as it leaves the light source.

• A directional light is located infinitely far away from the scene; consequently, its light rays are parallel.

• A positional light is located at some exact position within the scene. A positional light radiates light in all directions from the source unless it is defined as a spotlight.

• A spotlight is a positional light whose light output is restricted to a cone. The cutoff determines the width of the cone, and the falloff determines its concentration, that is, the light intensity across a plane that intersects the cone at right angles to its axis (Figure 5)..

• Latitude and longitude are defined as for the earth. Values towards the "north" and "east" are positive; those towards the "south" and "west" are negative. The radius is defined from the center of the viewing sphere.

• Real light is attenuated, meaning that its intensity decreases as the distance from the light source increases. Light attenuation is simulated by multiplying the intensity of light from a given source by an attenuation factor:

  

where d = distance between the light and the object, k_c = a constant, k_l = the linear attenuation factor, and k_q = the quadratic attenuation factor.

Attenuation applies only to positional lights, since they are located at a defined distance from the scene.

The book by Neider et al. (1993) contains a good discussion of lighting that can help in understanding and using the Cerius² lighting controls.

Accessing the tools

Select the View/Graphics/Lighting... menu item to access the Lighting control panel. Unless you also have a solid surface displayed, make sure your model is displayed in some style other than stick or trace (Atom and bond display styles), since lighting has no effect on lines or points.

Tip

Example

A tutorial example of using the lighting controls to illuminate a model is found under Lighting your model.

Additional information

Please see the on-screen help for details on the functioning of each control in the control panels mentioned in this section.

Adjusting global light settings

To light both the inside and outside of models displayed in cylinder style (Bonds as cylinders) or both sides of solid surfaces (e.g., such as those produced with one of the quantum chemistry modules), check the Two Sided Lighting check box. (This control has no effect with ball or ball-and-stick display styles.)

Viewing position

To change your virtual viewing position, check or uncheck the Local Viewer check box. Depending on the type of model, display style, and light position(s), the model may or may not look better with local viewing. However, graphics speed can be noticeably slower with Local Viewer enabled.

Ambient light

To change the brightness of the ambient light, adjust the Gray control. This affects only the global ambient light, which does not have any discrete light source.

To use a colored ambient light, use the red, green, and blue sliders (or the entry boxes below them) to set the proportions of red, green, and blue.

To return to a neutral-colored ambient light, click or adjust the Gray control.

Defining discrete light sources

Preliminary activities

First, choose which light source to define or redefine from the Light popup on the Lighting control panel (see Accessing the tools) and check the Enabled check box to turn it on. Turn off other lights if you want to see the effects of only the light you are defining.

Finding information

This section includes information on:

Color and components

Directional lights

Positional lights

Spotlights

Light attenuation

Accessing the tools

Click the Color... pushbutton on the Lighting control panel to access the Lightsource Colors control panel.

Brightness and color of ambient, diffuse, and specular components

To change the brightness of the Ambient, Diffuse, and Specular components of your light source, adjust the appropriate Gray control in the Lightsource Colors control panel.

To adjust the colors of the Ambient, Diffuse, and Specular components of your light source, use the appropriate red, green, and blue sliders (or the entry boxes below them) to set the proportions of red, green, and blue.

To return the Ambient, Diffuse, and Specular components of your light source to a neutral color, click or adjust the appropriate Gray control.

How it works

In general, the ambient component affects the contrast (how flat or 3D the model appears), and the relative amounts of the specular (highlighting) and diffuse components affect how shiny or matte the object appears (see Concepts for more details).

Directional lights

Accessing the tools

To set up a directional light (located at infinity), click the Position... pushbutton in the Lighting control panel to access the Lightsource Position control panel.

Select the Light is Directional control.

Changing the direction of illumination

You can change the direction from which the light illuminates the model by using any combination of the X, Y, Z, Latitude, and Longitude controls (the Radius control is ignored, since the a directional light is, by definition, located at infinity).

How it works

For example, you can:

• Illuminate from directly in front of the computer screen by setting the X and Y directions to 0 and the Z direction to any positive number.

This is equivalent to setting the Latitude and Longitude both to 0.0°.

• Illuminate from the lower right front by setting the X and Z directions to positive values and the Y direction to a negative number.

The absolute values of these numbers are unimportant since you are a defining only a direction, not a position; however, their ratios do affect the direction.

• Move the light source upwards by increasing the value of the Latitude.

• Swing it around to the left by decreasing the Longitude.

• Illuminate from directly behind your model by setting the X and Y directions to 0 and the Z direction to a negative number.

This is equivalent to setting the Latitude to 0.0° and the Longitude to 180°.

Accessing the tools

To set up a positional light (located within the scene), click the Position... pushbutton in the Lighting control panel to access the Lightsource Position control panel.

Select the Light is Positional control.

Changing the location of the light

You can change the light's location by using any combination of the X, Y, Z, Latitude, Longitude and Radius controls.

How it works

You can, for example:

• Illuminate from a light positioned directly to the right of your model by setting Y and Z to 0.0 and X to a number (in angstroms) beyond the right side of your model (say, 10 Å for a small-molecule model).

This is equivalent to setting Latitude to 0.0°, Longitude to 90°, and the Radius (in angstroms) to the value used for X.

• Position the light in the lower right forward quadrant of the scene by setting Latitude to about -30°, Longitude to about 80°, and Radius as needed to produce the desired effect (perhaps 10 Å for a small-molecule model).

• Provide backlighting by increasing the absolute Longitude beyond 90° (or -90°) or by using a negative value for Z.

• Illuminate at the position of an atom by pressing <Shift> on the keyboard and clicking the atom with the right mouse button to obtain an information window that includes its Cartesian coordinates (this information is also printed in the text window). Enter these values as the X, Y, and Z values. You can then pull the light away from the model by increasing the Radius.

Tip

Spotlights

Accessing the tools

To convert a positional light (Positional lights) into a spotlight and adjust the spotlight, click the Spotlight... pushbutton in the Lighting control panel to access the Spotlight Settings control panel.

Width of the spotlight

To control the width of the spotlight, adjust the Cutoff control. A value of 180° means the positional light is not a spotlight, and only cutoff values between 0° and 90° have any meaning (see Figure 5).

Tip

Aiming the spotlight

To illuminate the model, a spotlight not only has to be located at the desired position (as defined and displayed in the Lightsource Position control panel, Positional lights) but also needs to be pointed in the correct direction.

To adjust the direction in which the spotlight shines, use the Spotlight Direction controls in the Spotlight Settings control panel. You would generally want the direction to proceed from the position of the spotlight towards the model.

You might want to start your adjustments by setting the spotlight's latitude to the negative of its positional latitude and the spotlight's longitude to its positional longitude plus 180° (subtract the resulting longitude from 360 if it is greater than 180, since the value entered must be < |180|). You may also want to increase the Radius of the spotlight's position (using the Lightsource Position control panel) to illuminate the entire model.

Final adjustments

Then you can narrow the cutoff, and iterate using the Cutoff and Spotlight Direction controls (in the Spotlight Settings control panel), as well as the position controls (in the Lightsource Position control panel), until the light shines exactly where you want it.

To make the illuminated area gradually fade into the nonilluminated area of your model, you can increase the Falloff value. Larger values make the light relatively more intense near the center of the light cone and smooth the transition from the light to the dark area.

Related information

If the edges of the illuminated area appear too jagged, you can increase the display resolution (see Object resolution).

Light attenuation

Accessing the tools

Click the Attenuation... pushbutton in the Lighting control panel to access the Lightsource Attenuation control panel.

Adjusting the attenuation

To make the relative brightness a linear function of the distance of an object from the light source, enter a nonzero value for the Linear factor.

To make the relative brightness a square function of the distance of an object from the light source, enter a nonzero value for the Quadratic factor.

To uniformly make the illumination dimmer or brighter, adjust the Constant control.

Rendering and ray-tracing

How RayTrace works

Regardless of the display style that you have selected, RayTrace uses the ball display style (Atoms as balls) and the currently defined default element colors to render atoms as van der Waals spheres. The lighting controls (Lighting control) do not affect ray tracing at this time.

The rendered image appears in a separate Cerius² window called the Cerius2 Ray Tracing window. The bitmapped image displayed in this window cannot be manipulated or printed. However, you can use a third-party screen-capture utility or print utility to capture or print the rendered image. You can also save the intermediate files that are used in producing the ray-traced image.

How PSYCHO works

PSYCHO produces an encapsulated PostScript file and enables more flexibility than RayTrace in defining the output. PSYCHO reads atom and bond information and can generate color or gray-scale images of spheres, cylinders, and polyhedra and can label atoms with any text strings. PSYCHO also plots any isosurfaces that are present on the model (such as orbitals), although this creates significantly larger output files.

The final PSYCHO image is generally similar to the image in the Cerius² model window, although it does not include (for example), bond orders, hydrogen bonds, custom pen colors, or custom lighting effects.

When you render a PSYCHO image, Cerius² creates a PSYCHO input file (default name = C2Psycho.dat) and then runs PSYCHO with appropriate options. PSYCHO reads the input file and creates a PostScript file (default name = C2Psycho.eps or C2Psycho.ps), which by default is automatically previewed on your machine's PostScript previewer. If you like what you see, you can then send the PostScript file to your PostScript printer, through your previewier or via the Cerius² File/Print... menu item (Printing models and graphs).

The Cerius² PSYCHO control panels also give you access to the PSYCHO input file and options so that you can experiment with more complex PSYCHO renderings.

Accessing the tools

Select the View/Rendering... menu item to access the Render Models control panel. Click the Preferences... pushbuttons on that control panel to access the Psycho Preferences and Raytrace Preferences control panels.

Rendering models

Use the Render Models control panel to specify the model(s) and atoms that you want to be rendered, as well as the rendering method.

For raytracing, you may want to change how shiny or dull the atoms appear and how jagged or fuzzy the image appears by using controls in the Raytrace Preferences control panel. You can also use this control panel to specify that the intermediate files be saved and to give them a common root name.

For PSYCHO, you can use the Psycho Preferences and More Psycho Options control panels to set many available options.

Click the RENDER pushbutton in the Render Models control panel to start the rendering process.

Depending on your computing power, the rendering process may take some time. (There may also be a delay before the model reappears, if you move the Cerius2 Ray Tracing window.)

To close the Cerius2 Ray Tracing window, click anywhere in it.

Additional information

Please see the on-screen help for details on the functioning of each control in the Render Models, Raytrace Preferences, Psycho Preferences, and More Psycho Options control panels.

Stereo viewing

Accessing the tools

Select the View/Graphics/Stereo... menu item to access the Stereo control panel.

Specifying stereo display

Two stereo viewing methods are available, each producing dual images of the current model (or models, if in overlay mode, see Controlling model visibility and the display mode) in a slightly different orientation:

• To use the Crystaleyes stereo hardware and glasses from StereoGraphics Corporation (marketed by Silicon Graphics, Inc. as Stereo View), set the STEREO CONTROLS to CRYSTALEYES and select STEREO.

• To use an ordinary stereo viewer or view in stereo by crossing your eyes, set the STEREO CONTROLS to STEREO-PAIR and select STEREO.

For viewing with a stereo viewer, set the popup to DISTAL.

For viewing cross-eyed, set the popup to DISTAL or PROXIMAL, whichever works for you. (In distal mode, the left-eye image is on the left side of the screen and the right-eye image on the right; in proximal mode, the images are reversed.)

Adjust the Stereo Separation control to optimize your comfort and ease in interpreting the model. The separation affects the apparent flatness or three-dimensionality of the model.

Keyboard shortcuts

To toggle between mono and stereo display, press <F4>.

To toggle between Crystaleyes and stereo-pair modes, press <F5>.

To adjust the separation, drag the mouse in the model window while holding down <Shift> and <Alt> and the right mouse button.

Note

Related information

You may find that the stereo option works better for you if you view the model in perspective projection (Projection).

Additional information

Please see the on-screen help for details on the functioning of each control in the Stereo control panel. Mouse functions and keyboard shortcuts are summarized in Mouse and Keyboard Actions.