Cerius2 Modeling Environment



8       Viewing and Displaying Models

 The Cerius2·Visualizer allows you to position models as desired, to move models relative to one another, and control how models are displayed and printed. You can also annotate them with labels and arrows, etc., and animate models according to the results of certain calculations.

This section explains

This section tells you how to accomplish:

Moving models on the screen

Animating models

Labeling and annotating models

Model display style

Resolution and graphical quality

Printing models and graphs

Table 6. Finding information about viewing models

If you want to know about: Read:
Mouse buttons and keyboard use.   Mouse and Keyboard Actions.  
Rotating, moving, and magnifying the model view.   Moving models on the screen.  
Moving parts of models.   Editing the structure.  
Transferring models or parts of models between model spaces.   Moving models between model spaces.  
Docking models.   Moving models relative to one another.  
Superimposing models (rms matching).   Superimposing models.  
Continuous rotation or rocking of models.   Changing the default mouse rotation action.  
Scaling the view.   Changing the view magnification.  
Size of the model window.   Maximum size.  
Centering or resetting the model display.   Setting position and orientation.  
Screen coordinates.   Figure 3. Window axes in Cerius2 model window.  
Z-clipping.   Cross sections of models.  
Kekule or resonant display of phenyl rings.   Bond order display.  
Space-filling models.   Atoms as balls.  
Structural display of charged inorganic systems.   Cations as polyhedra.  
Thermal motion of atoms.   Thermal ellipsoids.  
Adding lines, boxes, circles, etc. to display.   Custom annotations.  
Labeling models with geometric measurements   Measuring models.  
Viewing close contacts.   Calculating close contacts.  
Controlling colors used in displaying models.   Model display colors.  
Changing the display and print resolution.   Resolution and graphical quality.  
Other advanced control of model rendering and lighting.   Enhancing Model Display.  
Displaying Connolly surfaces.   Model surfaces.  
Changing the display of model surfaces.   Surfaces--style and transparency.  

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) a model and should know how to select atoms in your model (Selecting atoms and groups of atoms).

If your session contains several models, you should know how to specify the current model (Specifying the current model). You may also want to know how to select atoms in several models (Selecting atoms in several models).


Moving models on the screen

Changing the position, viewing angle, and magnification of models in the model window aid in tasks such as accessing parts of the model, viewing small parts of the model in detail, understanding the model's 3D structure, bringing related or complementary models together in space, optimizing displays for printout.

Finding information

This section includes information on:

Basic tasks and methods

Moving models relative to one another

Superimposing models

Storing and retrieving views

Related information

Moving parts of models is discussed under Editing the structure. Copying models or parts of models from one model space to another is discussed under Moving models between model spaces.

Basic tasks and methods

Basic model-viewing tasks can often be accomplished in several ways: by using the mouse in the model window, using tools in the toolbar of the Cerius2·Visualizer's main control panel, using control panels accessed from menu items in the main control panel (mainly from the View menu), or using keyboard shortcuts. The various methods differ in convenience, quickness, and/or accuracy.

Note

The basic model viewing tools do not alter the original coordinates of the models. They affect only the view and appearance of models in the model window.  

Finding information

Basic model-viewing tasks affect all models and include:

Translating models

Rotating models

Changing the view magnification

Setting position and orientation

Display axes

You rotate and translate models relative to the x, y, and z display (window) axes, which are always oriented as shown in Figure 3. (These window axes are not the same as the model's viewing-angle axes, which are usually displayed in the lower right corner of the model window, see Default annotation.)

Figure 3 . Window axes in Cerius2 model window

The z axis points perpendicularly out of the computer screen.  

Example

A tutorial example of basic model moving is found in Moving a model.

Translating models

Manual translation

To interactively translate models, place the cursor in the model window and then press the middle mouse button and drag the mouse in any direction within the xy plane.

Incremental translation

Select the View/Dials... menu item to access the Viewing Dials control panel.

To move the models in an x or y direction, use the arrow tools in the Pan controls.

To return the model to its original position, click the reset button (in the center of the arrow tools).

Additional information

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

Rotating models

Manual rotation

To interactively change the viewing angle of models, place the cursor in the model window and then:

Tip

The default mouse behavior described here can be altered by changing the mouse rotation action from normal to continuous or rock (see Changing the default mouse rotation action).  

Changing the default mouse rotation action

To change the default way in which mouse-driven rotations behave, select the View/Options... menu item to access the View Options control panel. Choose the desired function under Mouse Rotate Action. The available modes are:

Large rotations

To quickly change the viewing angle in large steps, place the cursor in the model window and then:

Continuous rotation

Select the View/Dials... menu item to access the Viewing Dials control panel.

To continuously rotate the models about the x, y, or z axis, click and hold a slider or click and continuously drag a dial pointer.

Precise rotation

Select the View/Dials... menu item to access the Viewing Dials control panel.

To rotate the models to a specific angle about the x, y, or z axis, drag the sliders, click any point on the dials, and/or enter angles (in degrees) in the entry boxes. Dragging a slider is the least exact of these methods, and entering an angle, the most.

Orienting according to atom positions

You can orient the view so that selected atoms in the current model lie parallel or perpendicular to the computer screen.

To do this, select the View/Orient... menu item to access the Orient View control panel. Select the desired atoms. Click the Parallel To Screen or Perpendicular To Screen action button. (All visible models rotate in concert, around the same axis and by the same angle.)

The model view is reoriented so the best-fit plane through the selected atoms is lies in or perpendicular to the plane of the computer screen.

Additional information

Please see the on-screen help for details on the functioning of each control in the Viewing Dials, Orient View, and View Options control panels. Mouse functions and keyboard shortcuts are summarized in Mouse and Keyboard Actions.

Changing the view magnification

Manual zooming

To interactively change the view scaling of models, you can place the cursor in the model window and:

or:

Moving the cursor up and/or to the right increases the magnification; moving it down and/or to the left decreases magnification.

Filling the model window

To shrink or expand the view so that the models almost fill their model window pane(s), you can do any of:

Maximum size

To obtain the largest viewing area possible, you can change the size of the model window.

To enlarge the model window so that it fills the computer screen, you can do any of:

Normal model window size

To return the model window to its usual size, you can:

or:

Incremental zooming

To change the view scaling of the models in increments, you can place the cursor in the model window and:

or:

To zoom into or out of the models, use the arrow tools in the Magnification controls.

To return the models to their original magnification, click the reset button (between the arrow tools).

Continuous zooms

Select the View/Dials... menu item to access the Viewing Dials control panel.

Click and hold one of the Magnification arrow tools.

Precise magnification

Select the View/Dials... menu item to access the Viewing Dials control panel.

Enter a value in the Magnification entry box. Values greater than 1.0 enlarge the display. Values less than 1.0 shrink the display.

Additional information

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

Setting position and orientation

Topics in this section include: resetting the view of the models to the default position, orientation, and magnification; centering the display (the differences between centering and resetting are presented in this section); and defining a center of rotation for the current model.

Resetting the view

Resetting changes the viewing angle so that the model's x, y, and z axes are coincident with the window x, y, and z axes. Any translations are reversed by returning the model to the origin, and the magnification is returned to unity.

To reset the view of the models, you can do any of:

Defining the center of rotation

The center of rotation of a model is the centroid of all or selected atoms. By default, all atoms are used. To redefine the center of rotation for the current model, select the desired atom(s). (Selecting no atoms is the same as selecting all atoms.) Then you can do any of:

Centering the model

Centering a model translates it so that its center of rotation is in the center of the screen. Centering does not change the viewing angle or magnification. Centering immediately after defining the center of rotation (see Defining the center of rotation) affects only the current model. Centering after some other change in the model view moves all models in concert.

To center the model(s), you can do any of:

Any nondefault definition of the center of rotation is cancelled by such actions as resetting the view (Resetting the view) or filling the window (Filling the model window).

Additional information

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

Moving models relative to one another

You can move one model relative to another, for example, to investigate how a ligand fits in a receptor site.

Although the models technically occupy separate model spaces, this functionality allows the models to behave as if they have been redefined as submodels constituting one model in one model space.

Accessing the tools

Select the Move/Model Move... menu item to access the Model Space Transforms dcontrol panel. The current model is the one that is rotated and/or translated.

Alternatively, you can use mouse-keyboard combinations to control movement of the current model.

Bringing two models into one conjoined space

Simply make the desired models visible (Controlling model visibility and the display mode). Using the overlay display mode (Controlling model visibility and the display mode) and hiding any models you are not currently working with (Controlling model visibility and the display mode) should be most convenient; however, any display mode may be used.

Specifying the current model

Use any of the conventional means of defining a model as current (Specifying the current model).

Translating the current model

To translate the current model, you can:

or:

Specifying the translation axis

You can define a translation direction by entering a value in the Translate/Rotate Axis entry box or selecting some atoms and then clicking the associated DEFINE pushbutton in the Model Space Transforms control panel.

Rotating the current model

The rotation axes are the display axes, as shown in Figure 3.

To rotate the current model, you can:

or:

Specifying the center of rotation

You can define the center of rotation and rotation axis by entering values in the Rotation Center and Translate/Rotate Axis entry boxes or selecting some atoms and then clicking the associated DEFINE pushbuttons in the Model Space Transforms control panel.

Saving the model with its transformed coordinates

When you save the model in .msi format (Saving model structure files), both its original coordinates and the transform for generating the transformed coordinates are automatically saved.

Additional information

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

Superimposing models

You can superimpose (or "match") models by performing a least-squares fit between selected atoms. Whole (nonperiodic) models or the asymmetric unit of periodic models can be superimposed. One model is translated and rotated as a rigid unit to obtain the best rms fit of the selected atoms with those of a reference (or target) model. This is useful for comparing structures of all or parts of models.

Accessing the tools

Select the Move/Atoms Match... menu item to access the Match Models control panel.

Specifying the models

Specify which model is the reference model and which is the movable model by selecting them from the pulldowns or typing their model numbers or names in the text entry boxes.

Specifying the atoms to superimpose

The number of atoms specified in the reference model must be the same as the number in the moving model.

If you want to take all atoms into account during the fitting, the models must have the same number of atoms and they must be numbered identically (you can label a model according to atom numbers, see Labels). If this is true, you don't need to select atoms in order to specify them.

If you want or need to select the atoms to be matched, select them in the same order in both models. If atoms in the two models are numbered identically and you want to superimpose identically numbered atoms, you need select atoms only in one model.

Performing the superimposition

You can mass-weight the calculation (for example, if the positions of hydrogens are less important) by setting the atom weighting popup to MASS.

Be sure that all desired atoms are still selected, then click the MATCH pushbutton to superimpose the models and report the rms fit in the text window.

Additional information

Please see the on-screen help for details on the functioning of each control in the Match Atoms control panel. Selecting atoms in more than one model is discussed in Selecting atoms in several models.

Related information

The Cerius2·Align Molecules module (which is separately licensed and documented and is typically found in the DRUG DISCOVERY deck of cards) offers additional functionality for comparison of model structures.

Storing and retrieving views

You can save the current view (that is, the model and its viewing conditions such as orientation, location, magnification) in memory for later retrieval during the current session. Up to ten views can be saved and retrieved for later viewing within the current session.

Storing a view

To store a view, select the View/Orient... menu item to access the Orient View control panel. Set the View A-J popup as desired and click the STORE pushbutton.

Retrieving a view

To retrieve a view, select the View/Orient... menu item to access the Orient View control panel. Choose the desired view from the View A-J popup and click the RETRIEVE pushbutton.

Additional information

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


Animating models

The Visualizer animation facilities enable you to create an animation sequence from a trajectory file (such as that produced by the Cerius2·Dynamics Simulation module), and then replay that sequence using VCR-style controls.

You should already know...

How to produce trajectory files is discussed in the documentation for the relevant application modules (which are purchased separately).

The animation process

Animating a model is a three-stage process. You first need to select a trajectory (.trj) file and load the information from it. Next you build an animation sequence. (Alternatively, check the Automate Build check box before loading the file.) Finally, the model is animated by "playing back" the animation sequence.

Accessing the tools

Select the View/Animation... menu item (on the main control panel's menu bar) to access the Animation control panel.

Loading a trajectory file

Use the file browser and selector tools to choose the trajectory file from which to construct the animation sequence. How to use these tools is detailed under Loading model structure files. (All file browsers work similarly.)

If the trajectory file you request appears to be associated with the current model, Cerius2 asks if you want to use this model as the initial frame of the trajectory. Otherwise, Cerius2 loads the associated MSI-format model file as the current model.

Building an animation sequence

To build an animation sequence that uses all frames from a trajectory file, simply check the Automate Build check box before selecting the trajectory file.

To use only selected frames from the selected trajectory file, click the Frame Filter... pushbutton to access the Frame Filter control panel. Use this control panel to select a subset of the frames: you can specify the starting and ending frame numbers and the frame increment. Then click the BUILD FRAMES pushbutton in the Animation control panel.

Animating the model

Once the desired frames have been built into an animation sequence, you can use the Replay Animation controls to animate the model by replaying all or specified frames. These controls operate similarly to those on a tape recorder or VCR.

You can use other controls during or before the animation, for example, you can change the viewing angle (Rotating models), magnification (Changing the view magnification), or display style (Atom and bond display styles).

Clearing memory

Animation sequences consume a considerable amount of memory. When you have finished with a sequence, you should clear the memory buffer in which it is held, by clicking the Clear All Frames action button in the Animation control panel.

Additional information

Please see the on-screen help for details on the functioning of each control in the Animation and Frame Filter control panels.


Labeling and annotating models

Why read this section

Cerius2 allows you to label atoms according to various properties such as element names, atom type, charge, temperature, hybridization, etc. You can also annotate models by adding text and graphical objects such as arrows and boxes. In addition, the default type of annotation that Cerius2 always shows in the model window can be changed.

These functions are useful for understanding the displayed model and for enhancing the appearance of models for presentation and display purposes.

Finding information

This section includes information on:

Labels

Default annotation

Custom annotations

Related information

You can also enhance model displays by, for example, coloring atoms according to various properties (Model display colors) or color-mapping properties onto model surfaces (in, for example, the quantum chemical application modules, which have separate documentation).

Labels

Labels can be applied to entire models (when all or no atoms are selected) or to selected atoms within one or more models. Different labels may be used for different parts of a model.

The following label properties are available:

NO LABEL
No labels

NUMBERS
Atom serial numbers

SYM/NUM
Crystal symmetry copy plus atom serial numbers

ELEMENTS
Element types

CHARGES
Atom partial charges

FORMAL CHARGE
Atom formal charges

OCCUPANCY
Atom site occupancies

ISOTROPIC
Atom isotropic temperature factors

FFYTPE
Forcefield atom types

HYBRID
Atom hybridization

NAME
Atom name

MASS
Atom mass

CHIRALITY
Atom chirality

Adding, changing, or removing labels on atoms

To add, change, or remove labels on all or selected atoms, you can:

or:

Tip

You can interactively query the current properties of an atom by shift-clicking the atom with the right mouse button. A message box appears that lists the coordinates and properties of the atom.  

Labeling bond attributes

Bonds can be labelled with their fractional bond orders.

To add or remove labels on all or selected bonds, you can:

Example

A tutorial example of labeling a model is found in Labeling a model.

Additional information

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

Related information

Measuring distances, angles, planes, torsions, and inversions for the atoms in a model and displaying these measurements in the model window is discussed under Measuring models.

Default annotation

Basic information that is usually shown by default comprises the model name and model space number (in the lower left corner of the model window) and a small set of axes indicating the viewing angle (lower right corner). You may hide this information if you prefer.

In addition, you may want to show a scale bar and/or a large set of axes in the model window.

Accessing the tools

To change the default information shown in the model window, select the View/Options... menu item to access the View Options control panel. Check or uncheck the appropriate View Annotation check boxes.

Additional information

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

Custom annotations

Accessing the annotation tools

Select the Build/Annotation... menu item to access the Annotation control panel.

Annotating your model

The Annotation control panel contains several types of tools to help you highlight and enhance your displayed model:

To add lines to the model display, you use the Line tool.

Select the Line tool, then click the left mouse button in the model window to place one end of the line. Without releasing the mouse button, drag the line out by moving the cursor, then release the mouse button to place the other end of the line.

The new line uses the currently set annotation color and line width (see Editing the annotation objects).

To add arrows to the model display, you use the Arrow tool.

Select the Arrow tool, then click the left mouse button in the model window to place the tail of the arrow. Without releasing the mouse button, drag the arrow out by moving the cursor, then release the mouse button to place the head of the arrow.

The new arrow uses the currently set annotation color and line width (see Editing the annotation objects).

To add rectangles or squares to the model display, you use the Rectangle tool.

Check the Filled check box if you want a filled rectangle; assure that it is unchecked if you want an outline rectangle.

Select the Rectangle tool, then click the left mouse button in the model window to place one corner of the rectangle. Drag the rectangle out by moving the cursor, then release the mouse button to place the opposite corner of the rectangle.

The new rectangle uses the currently set annotation color and line width (see Editing the annotation objects). For filled rectangles, the fill color is the same as the outline color.

To add circles to the model display, you use the Circle tool.

Check the Filled check box if you want a filled circle; assure that it is unchecked if you want an outline circle.

Select the Circle tool, then click the left mouse button in the model window to place the center of the circle. Drag the circle out by moving the cursor, then release the mouse button to place the circle.

The new circle uses the currently set annotation color and line width (see Editing the annotation objects). For filled circles, the fill color is the same as the outline color.

To add text to the model display, you use the Text tool.

Specify the text content by entering it in the entry box to the right of the Text tool. Then select the Text tool and click the left mouse button in the model window to place the text annotation.

The new text annotation object uses the currently set text content, annotation color, font, style, and size (see Editing the annotation objects).

Editing the annotation objects

You can use the annotation tools discussed in this section in two ways:

To set or change the color of any annotation object, use the color popup (to the right of the Line tool in the control panel). Additional color controls can be accessed by clicking the More Colors... pushbutton. This brings up the Color Selected Objects control panel (see Model display colors).

To specify that rectangles or circles be drawn in filled or outline style, check or uncheck the Filled check box. The fill color is always the same as the outline color.

To set or change the line width of an annotation object (except for text), enter a number in the Line Width entry box.

To set or change the properties of text annotation objects:

Moving, resizing, and removing annotations

You can move, change the size of, delete, or hide annotation objects:

Recovering from mistakes

An UNDO pushbutton, provided at the top of the control panel, can be used to cancel one or a series of previous commands for many types of operations. The UNDO button is greyed out when there is nothing to cancel.

Help

Checking the Guide? check box gives you on-screen help (in the upper left corner of the model window) on the Annotation control panel functions.

Additional information

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


Model display style

Why read this section

You can change the model display to suit your needs. For example, you may want to display molecules in traditional stick style or with ellipsoids representing thermal movements of atoms, you may want to emphasize some atoms, or you may want to view a cross section of a model.

Finding information

This section includes information on:

Atom and bond display styles

Structure traces

Cross sections of models

Apparent depth effects

Related information

Labeling atoms according to various properties is discussed under Labels. Setting the graphical quality and screen resolution is discussed under Resolution and graphical quality.

You can also enhance model displays by, for example, coloring atoms according to various properties (Model display colors) or adding Connolly (Model surfaces) or other surfaces.

Atom and bond display styles

Display styles can be applied to entire models (when all or no atoms are selected) or to selected atoms within one or more models. Different display styles may be used for different parts of a model.

Finding information

This section includes information on displaying:

Bonds as sticks

Bond order display

Bonds as cylinders

Lone atoms

Atoms as balls

Ball and stick models

Cations as polyhedra

Thermal ellipsoids

Example

A tutorial example of changing model display styles is found under Changing the display style.

Additional information

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

Bonds as sticks

Understanding the display

The default is to display bonds as single, double, or triple lines. Atoms are not specifically shown, but are present at the ends of bonds. The bond colors represent the element types of the atoms at each end.

Specifying stick style

To reset stick display style, you can:

or:

Bond order display

 Understanding the display

Multiple bonds can be shown as a set of parallel lines representing the bond order. Partial-double bonds in 6-membered ring systems can be represented as (both displayed and stored with the model as) Kekule or resonant bonds (Figure 4).

Figure 4 . Representation of partial double bonds in 6-membered rings

Left: Kekule representation of benzene; right: resonant-bonds representation.  

In addition, all bonds can be displayed as single lines regardless of the bond order (and without changing the actual bond order). This is useful, for example, for simplifying the display when viewing large models at small magnification. It does not change the actual bond type, which is stored with the model.

Specifying partial double bond style

To set the representation of partial double bonds to resonant (dashed lines) or Kekule (alternating single and double bonds), you can:

or:

Specifying multiple bond style

To display all bonds (in all models) as single lines (regardless of actual bond type), select the View/Display Attributes... menu item to access the Display Attributes control panel. Click the Preferences... pushbutton to access the Style Preferences control panel. Uncheck the Highlight Multiple Bonds check box.

To display the bond types again, simply check the Highlight Multiple Bonds check box.

Bonds as cylinders

Understanding the display

Cylinder style is similar to stick style, except that the bonds are represented by cylinders, providing a more three-dimensional representation. Atoms are not specifically shown, but are present at the ends of bonds. The bond colors represent the element types of the atoms at each end.

Specifying cylinder style

To display bonds in cylinder style, you can:

or:

Setting the radius

To set the radius of the cylinders, click the Preferences... button in the Display Attributes control panel to access the Style Preferences control panel. Enter the desired radius in the Cylinder Radius entry box.

Lone atoms

Understanding the display

Lone (not bonded) atoms in a model can be represented as three-dimensional crosses, small spheres, or simple points or can be not displayed at all.

Specifying lone-atom style

To change how lone atoms are displayed, select the View/Display Attributes... menu item to access the Display Attributes control panel. Click the Preferences... button to access the Style Preferences control panel. In the latter control panel, set Lone Atom Style to CROSS, BALL, POINT, or NONE.

Atoms as balls

Understanding the display

Atoms can be represented by space-filling balls. If any bonds are visible between balls, they are represented as lines.

Specifying ball style

To display atoms in ball style, you can:

or:

Setting the radii

The ball radii are proportional to the van der Waals radius of the respective atoms. To set the ratio of ball radius to van der Waals radius, click the Preferences... pushbutton in the Display Attributes control panel to access the Style Preferences control panel. Enter the desired proportion in the Ball: Ball Size entry box.

Ball and stick models

Understanding the display

Ball and stick style represents atoms as van der Waals spheres and by bonds as cylinders.

Specifying ball-and-stick style

To display models in ball and stick style, you can:

or:

Setting the ball radii

The ball radii are proportional to the van der Waals radius of the respective atoms. To set the ratio of ball radius to van der Waals radius, click the Preferences... pushbutton in the Display Attributes control panel to access the Style Preferences control panel. Enter the desired proportion in the Ball & Stick: Ball Size entry box.

Setting the stick radius

To set the radius of the sticks, click the Preferences... button in the Display Attributes control panel to access the Style Preferences control panel. Enter the desired radius in the Stick Radius entry box.

Cations as polyhedra

Understanding the display

Polyhedra are used to simplify structural display for inorganic systems that contain tetrahedrally, octahedrally, or square- planar coordinated units, for example, zeolites, the high Tc superconductors, and multi-molybdates.

Solid coordination polyhedra are drawn around cations, the number of corners indicating the coordination number as defined by bonding connectivity.

Specifying polyhedral style

To display cations as polyhedra, you can:

or:

Displaying other atoms

Other atoms (non-cations) can be represented as crosses, small spheres, or single pixels or not drawn at all. To change how other atoms are displayed, click the Preferences... button in the Display Attributes control panel to access the Style Preferences control panel. Then set Non-Polyhedral Style to CROSS, BALL, POINT, or NONE.

Thermal ellipsoids

Understanding the display

Ellipsoid style represents a constant-probability surface for the thermal motion of the atoms. Atoms described by anisotropic temperature factors are represented by ellipsoids. (Atoms described by isotropic temperature factors are represented by spheres.) Lines representing bonds are drawn by default but can be removed. The orientation of the ellipsoid's principal axis may be displayed.

Spheres and ellipsoids are drawn only if the temperature factors describe a solid object. (In mathematical terms, the matrix must be positive definite.) If this is not true or if no temperature factor has been specified, atoms are represented by crosses.

Specifying ellipsoid style

To display atoms as thermal ellipsoids, you must first be sure that anisotropic temperature factors (see Understanding the display and Temperature factors) have been specified or loaded. Then you can:

or:

Displaying bonds and ellipsoid axes

To show or hide the principal ellipsoid axis, click the Preferences... pushbutton in the Display Attributes control panel to access the Style Preferences control panel. Check or uncheck the Show Principal Axes check box.

Similarly, to show or hide bonds, check or uncheck the Show Bonding check box.

Size of ellipsoids

You can define a scaling factor for the display size of thermal ellipsoids. A value of 1.0 corresponds to an ellipsoid whose radius at any point on the surface is equal to the root mean square (rms) atomic vibration in that direction. At a scaling factor of 1.0, the probability of the atom actually lying within the ellipsoid is low. Greater values produce greater probabilities, as shown in Table 7.

Table 7. Relation of thermal ellipsoid size to atom location

Scale factor Probability of atom being within ellipsoid
1.54   50%  
2.02   75%  
2.50 (default)   90%  
2.80   95%  
3.37   99%  

Setting the size

To set the scale factor for thermal ellipsoids, select the View/Display Attributes... menu item to access the Display Attributes control panel. Click the Preferences... pushbutton in the Display Attributes control panel to access the Style Preferences control panel. Enter the desired scale factor in the Ellipsoid Size entry box.

Structure traces

You can make only a structural trace of a model visible. This is done differently, depending on whether the model is a protein or any other kind of polymer.

Visibility of polymer backbones

To display only the backbone atoms of a polymer, select the View/Atom Visibility... menu item to access the Atom Visibility control panel. Click the Hide Non-Backbone Atoms action button. You must have previously defined some atoms as backbone atoms, using the Polymer Builder tools.

You can also use this control panel to hide hydrogen atoms or any selected atoms or to display all or selected atoms.

-carbon trace of proteins

To display an alpha carbon trace of a protein model:

or:

Additional information

Please see the on-screen help for details on the functioning of each control in the Atom Visibility and Display Attributes control panels.

Cross sections of models

You can control the apparent location of the viewing plane along a line perpendicular to the computer screen, as well as the plane's thickness, so as to view either the whole model or a cross section (slice or slab) through it. You do this by clipping the view between two coordinates of the screen z axis (that is, to set the apparent distance of the viewing plane from the computer screen).

Accessing the tools

To control and apply z-clipping, select the View/Graphics/Z-Clipping... menu item to access the Z-Clipping control panel. You can perform z-clipping in two ways:

Additional information

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

Apparent depth effects

Depth cueing

 Depth cueing gives models an appearance of depth by displaying objects that are apparently closer to the surface of the computer screen in true color and mixing the color with the background color for objects that appear to be farther behind the surface of the computer screen. The extent of depth cueing can be changed.

Accessing the tools

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

Adjusting the perceived depth

To adjust the degree of depth cueing, use the Depth Cue Factor slider or its associated entry box. A value of 1 means that apparently near and far objects are all drawn with full color intensity; a value of 0 means that far objects disappear into the background.

To change the apparent distances at which objects are drawn with full or minimal color, adjust the Near Distance or Far Distance controls, respectively.

Additional information

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

Projection

The projection method is another way of enhancing the appearance of depth in models. Two methods are available:

Accessing the tools

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

Adjusting the projection

Choose the desired projection method from the control panel. If you choose PERSPECTIVE, you can specify the projection angle by entering a number in the Angle entry box.

Alternatively, you can toggle the projection method by pressing <F3> on the keyboard. The perspective angle can be changed by dragging the mouse in the model window while holding down <Shift> and <Alt> and the middle mouse button.

Additional information

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


Resolution and graphical quality

Object resolution

The balls, ellipsoids, and cylinders produced by the various display styles are represented on-screen as multifaceted polyhedral facets (for balls and ellipsoids) and prismoidal facets (for cylinders). A small number of facets used to draw an object results in a fast but coarse display. Large numbers of facets improve smoothness and specularity, but at the expense of drawing speed. The default value usually provides a reasonable compromise between display speed and resolution.

Although the actual number of facets used is determined by the size of the object being represented, you can adjust their relative number. To do so, select the View/Display Attributes... menu item to access the Display Attributes control panel. Click the Preferences... pushbutton to access the Style Preferences control panel. Adjust the Resolution sliders by dragging or directly enter values in the associated entry boxes for Spheres, Cylinders, and/or Ellipsoids.

Line widths for bonds

To change the line width used to draw (non-cylinder) bonds, select the View/Display Attributes... menu item to access the Display Attributes control panel. Click the Preferences... pushbutton to access the Style Preferences control panel. Adjust the Line Width slider by dragging or directly enter values in the associated entry box.

Graphics quality

Cerius2 enables you to specify the quality of graphics displayed on the computer and written to vector PostScript files. Three quality settings are available: standard, better, and excellent. Higher quality settings reduce the golf-ball effect that results because X and vector PostScript triangles are flat-shaded instead of color-interpolated. However, each higher quality setting can also increase both the file size and the rendering time by a factor of four over the previous quality setting.

This quality setting is independent of the resolution settings for spheres, cylinders, and ellipsoids (Object resolution). This setting applies to the number of subdivisions made to simulate depth cueing of vectors, as well as to the number of subdivisions made to the triangles created during sphere, cylinder, ellipsoid, and surface tessellation.

To adjust the graphics quality, select the View/Display Attributes... menu item, then click the Preferences... button in the Display Attributes control panel. In the Style Preferences control panel that appears, set X/PostScript Quality to STANDARD, BETTER, or EXCELLENT. Each higher quality setting can increase both the file size and the rendering time by a factor of four over the next-lower quality setting.

Additional information

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


Printing models and graphs

Why read this section

This section includes information on:

You can print full-color, greyscale, or dithered black-and-white PostScript images.

PostScript files can be printed later. You can transfer them to other applications to edit them. They can also be imported into other applications, such as desktop publishing packages, for use as illustrations,

Related information

Setting the print resolution is discussed in Resolution and graphical quality. Using PSYCHO within Cerius2 for rendering models (and producing PostScript output) is discussed in Rendering and ray-tracing.

You should already know...

You need to know what UNIX print command (including command-line options) is usually used at your site for sending PostScript output from applications to a printer. Please ask an experienced user at your site, or your system administrator, if you do not know the command.

Accessing the tools

Select the File/Print... menu item to access the Print control panel. This contains the primary PostScript output controls and provides access to the Page Setup control panel, which contains supplementary controls.

Specifying what and how to print

Select the image source by setting Image Capture to Model Window or Graph Window. The size of the model window affects the image's detail when it is output as bitmap PostScript: the larger the window, the greater the detail. However, the size of the graph window does not affect the output detail.

Specify how you want the image to appear by setting Color to Full Color, Grayscale, or Black & White. Of course, your printer must be able to handle the selected color mapping.

Tell Cerius2 to send the output to a printer or a file by choosing the relevant PostScript Destination radio button. You can enter a filename in the entry box to the right of the FILE button. Specify the UNIX print command (including pathname, if needed, and command-line options) by entering it in the Command entry box.

Additional controls

You can access some less frequently used controls by clicking the Page Setup... pushbutton in the Print control panel, which causes the Page Setup control panel to appear.

Options on the Page Setup control panel enable you to adjust the presentation of the PostScript image to be generated. You can also scale the image, add legends, and fine-tune the output for maximum clarity. The controls available in this panel depend on how controls in the Print control panel are set.

Vector or raster format for printing model windows

If you are printing the image in the model window, you can choose to output in vector PostScript or screen dump (raster) format. Vector PostScript images are device-independent, can be resized without loss of display quality, and can produce better quality output (colors, shapes, and so on) on a PostScript printer. Raster images, such as screen dump images, may become distorted when they are scaled.

A vector PostScript file is often smaller than a screen dump file and, as a result, prints faster. However, if the image in the model window is very complicated or the display quality is high, a vector PostScript file can be larger than a screen dump file and may take longer to print.

Bitmap resolution for printing graphs

You can specify the resolution (in dots per inch) for curves in graphs. Increasing this value allows improved definition of these images, although the resolution of the output device is always a limiting factor. Increasing the resolution results increases the PostScript image generation time, file size, and printing time.

Previewing the output

If you run Cerius2 on an SGI platform, you can click the PREVIEW pushbutton in the Print control panel. This calls up SGI's xpsview utility, to preview your PostScript image before sending it to the printer or a file.

Printing or saving a PostScript file

Once all options have been set to your satisfaction, click the PRINT pushbutton in the Print control panel.

Example

A tutorial example of printing a model is found under Printing a model.

Additional information

Please see the on-screen help for details on the functioning of each control in the Print and Page Setup control panels. Changing the resolution with which graphics are displayed and written is covered under Resolution and graphical quality.



Last updated April 08, 1999 at 05:07PM Pacific Daylight Time.
Copyright © 1999, Molecular Simulations Inc. All rights reserved.