Cerius2 Modeling Environment

2       Introducing Cerius2

Why read this section

If you've never used Cerius² before, please go through this section first! The idea is just to get you familiar with using basic controls in the interface, then you can find details on how to use these and other controls for your own scientific problems in other sections.

If it's been a while since you've used Cerius² or you just want a quick summary of some basic activities, you may start with Starting Cerius2 and then skip to parts you find interesting.

This section includes instructions for:

Starting Cerius2

Building a model--caffeine

Saving a model

What you can do with a model display

Building another model--ferrocene

Reading in additional models

Managing multiple models

Printing a model

Controlling the 3D display

Exploring Cerius2 on your own

Prerequisites

• You need to have Cerius² already installed on your system (your own machine or an accessible machine on your in-house network).

Either you or you system administrator should have done this, with the help of the Cerius² Installation and Administration Guide.

• You need to know how to log in to your machine, how to get around in your directory structure, and the basics of managing your file system and working with your machine's user environment (see, for example, Todino & Strang 1990).

• You need a home directory in which you have write permission and can create subdirectories.

• You need to know how to start up Cerius² on your machine.

Whoever installed Cerius² at your site can tell you how to start it. If their instructions differ from those given under Starting Cerius2, please follow the instructions for starting Cerius² at your site.

In general, activities that you must perform if you want this tutorial to work as designed are contained in boxes like this.

Optional activities are in plain text (not in boxes).

Explanations of what you are doing are in italics.

Note

Additional information

Detailed information on how to carry out the activities introduced in this section (as well as other activities) is contained in the other sections of this documentation set.

Starting Cerius2

Starting in your home directory, you should first go to or make a subdirectory in which to run this tutorial. Do this by entering, for example, the following at your system prompt:

> cd > mkdir CeriusIntro > cd CeriusIntro

2.   Starting Cerius²

Enter at your system prompt: > cerius2

Cerius² is a large program, and it takes a few moments for it to load and appear on your screen. Additional information on starting Cerius² can be found under Starting Cerius2.

If an outline of a window attaches to your cursor instead of being placed on the screen, use the mouse to move the outline to the upper left corner of your screen and click there to place a large black window labelled Cerius2 Models.

If nothing happens

3.   Getting acquainted with the interface (optional)

Please feel free to take some time to explore the Cerius² interface on your own. You can't break anything!

Try using the left and right mouse buttons to click various buttons and other controls. If a list of items appears, continue to hold the left mouse button down and release it over an item to choose that item.

Try building or loading a model, if you want.

Important

Use the mouse to move the cursor over the File menu at the top left corner of the main control panel. Click with the left mouse button and drag the cursor down to New Session. Release the mouse button. When a small window labelled Re-initialize All... appears, click its Confirm button with the left mouse button.

Everything now goes back to its condition when Cerius² first loaded. If you moved any main windows, you should put them back to where they were when you started.

You can close any open control panel by left-mouse clicking in the box in its upper right corner.

Building a model--caffeine

The top of the Visualizer main panel contains a menu bar (a row of menus) that looks like this:

Use the mouse to move the cursor over Build in the menu bar. Press and hold down the left mouse button.

A list of menu items, or pulldown menu, appears:

Continue to hold the left mouse button down, use the mouse to drag the cursor downwards, and release the mouse button over the 3D-Sketcher... item in the list.

In other words

A window labeled Sketcher appears. This control panel contains basic model-building tools.

5.   Sketching the ring system of caffeine

You will not necessarily build caffeine in the quickest possible way, since we want to show how several different sketcher tools work.

Locate the template tool in the Sketcher control panel. It is labeled phenyl, since a phenyl ring is the default template.

The template tool looks like:

Use the mouse to move the cursor over the template tool and click once with the left mouse button.

In other words

The phenyl template tool changes color, indicating that it is active, and if you move the cursor into the large window, you will see that the cursor has changed to a T shape.

Move the cursor into the large window labelled Cerius2 Models.

Definition

This is called the model window.

Click once near the center of the model window.

A benzene fragment appears, but it is not oriented conveniently.

Move the cursor so it's near any edge of the model window. Then hold down the right mouse button and move the cursor parallel to the closest edge of the window until one of the double bonds is vertical and on the right side of the fragment.

The model should now look something like this:

Note

Click the Sketch with tool.

The Sketch with tool looks like:

The control panel indicates that you will sketch with C, whereas the ring you want to add contains 2 N's and only one C. So it might be more efficient to sketch with N instead of C:

Locate the popup control to the right of the Sketch with C entry box.

In other words, this control:

Click the popup control, then, while continuing to hold the left mouse button down, drag the cursor down and then release it over the N.

In other words

In the rest of this step, you will try to make your model look something like this:

In the model window, click the carbon at the top end of the double bond on the right side of the model.

You will hear a beep to confirm that you succeeded in hitting the atom.

Move the cursor up and towards the right.

A dashed line follows the cursor, connecting it with the atom you clicked and indicating where the bond to your next atom will lie.

Click in three places to the right of that double bond, then click the carbon atom at the bottom end of that double bond, forming a 5-membered ring that's fused with the 6-membered ring.

The new lines are blue-ish, indicating that all three atoms that you just added are nitrogens. The two carbons on the right side of the 6-membered rings now have too many bonds emanating from them. And the 5-membered ring might be oddly shaped. But don't worry--you'll correct these problems later.

If you make a mistake

If you really make a mess of your model, you can select the Edit/Select All menu item and then the Edit/Delete menu item to erase the entire model. Then start again at the beginning of Step 5.

6.   Adding R groups to the basic ring structure

Cerius² often offers several ways of accomplishing the same activity, allowing you to use whatever method you find convenient. We'll demonstrate two different ways of adding groups of atoms to a model. But first we'll show a different way of changing the atom that you'll be sketching with .

Click in the Sketch with text entry box.

The N becomes highlighted. Anything you type in the box will now replace the N.

Type a C in the Sketch with text entry box and either press <Enter> on your keyboard or click anywhere else on the control panel.

In other words

Click the bottom carbon in the 6-membered ring, then click below that carbon.

This adds a carbon, which will become a methyl group when you correct the hydrogens later.

(You may want to look at the picture of a complete caffeine model under Cleaning up the conformation for help in sketching your model.)

Here's another way of adding a methyl group:

Click the Templates... button in the Sketcher control panel.

The Templates... button looks like:

Clicking the Templates... button causes the Sketcher Template control panel to appear. This control panel contains a file browser that allows you to navigate among directories and load selected files.

In the Sketcher Template control panel, double-click organic/.

This opens the directory named organic and displays a list of the filenames that are inside that directory.

Now scroll down the items in the list of filenames by clicking below the slider on the scroll bar to the right of the list box. Stop when you see the filename methyl.

That is, click here:

You can also move the slider by clicking it, then dragging it down till you see the methyl filename.

Click methyl and then click the LOAD pushbutton.

The text next to the template tool in the Sketcher control panel becomes methyl, and the template tool is now active (highlighted).

In the model window, click the hydrogen atom that's attached to the carbon atom in the upper left part of the 6-membered ring. Next, click the uppermost N in the 5-membered ring.

Your model should now look approximately like this:

7.   Correcting the atom types

In the Sketcher control panel, find and click the Edit Element tool.

The Edit Element tool looks like:

The text entry box for this tool is already set to C.

Click the middle N in the chain of N's in the 5-membered ring.

The two half-bonds connected to this atom become grey, indicating that the atom has been changed to carbon.

Change the Edit Element type to O, by choosing O from the associated popup or by entering O in the Edit Element text entry box. Click the top H on the 6-membered ring.

Red indicates an oxygen atom.

Now click the bottom-left hydrogen that's directly attached to the 6-membered ring. Change the Edit Element type to N. Click each of the (two) carbons in the 6-membered ring to which the methyl groups are attached.

(Remember, the methyl group at the bottom of the 6-membered ring does not yet look like a methyl group.)

8.   Correcting the bond order

In the Sketcher control panel, find and click the Edit Bond tool.

The Edit Bond tool looks like:

The Edit Bond popup is already set to SINGLE.

Click one of the nitrogens in the 6-membered ring. Next click the carbon at the other end of the double bond that emanates from that nitrogen.

The double bond becomes a single bond.

Click the other nitrogen in the 6-membered ring, and then the carbon at the other end of its double bond. Now change the Edit Bond popup from SINGLE to DOUBLE. Click the bottom N in the 5-membered ring and the right-most carbon in the same ring. Click one oxygen and the carbon to which it is attached. Do the same for the other oxygen.

Your model should now look approximately like this:

(Still bad, but you're getting there!)

9.   Correcting the hydrogens

In the Sketcher control panel, click the H ADJUST button.

Now, except perhaps for some strange bond lengths or angles, your caffeine model is nearly finished.

10.   Cleaning up the conformation

Still in the Sketcher control panel, click and hold the CLEAN button until the model stops moving.

Now your model should be finished and look like:

Note

Click the selection tool (the arrow icon in the upper left of the Sketcher control panel) to return the cursor to its selection function.

Alternatively, you can simply close the Sketcher control panel, since you don't need it for a while. The cursor should now be a plain arrow when it's in the model window.

Saving a model

Now that you've built a model, you can save it:

Select the File/Save Model... menu item.

The Save Model control panel appears. If you named your working directory CeriusIntro as suggested in Step 1 and did not save any other files in this directory, the Save Model control panel should look like this:

Click in the text entry box next to the SAVE button. Change *.msi to caffeine.msi and click the SAVE button.

If you neglect to type the ".msi", Cerius² adds it automatically. The ".msi" helps you remember that the file is in Cerius²'s standard format.

12.   Cleaning up your screen

By now, you have several control panels scattered about your screen. You can close one control panel:

Closing control panels

Click the close button in the top right corner of any control panel.

Or you can close all open control panels at once:

Click the clear panels tool on the toolbar of the Visualizer main panel.

The toolbar is just below the menu bar and looks like:

(By now, you might want to relax and have a cup of real caffeine!)

13.   Interrupting this tutorial (optional)

If you need to quit your Cerius² session for any reason, you may do so now without losing any of your work.

To quit, simply select the File/Exit menu item and then click Exit in the Exit option... window that appears.

To resume this introduction to Cerius², cd to the directory that you made in Step 1 and start Cerius² as in Step 2.

To reload your caffeine model, select the File/Load Model... menu item. In the Load Model control panel's file browser, double-click (left mouse button) the name of the file that you saved in Step 11 (which should be caffeine.msi).

Close the Load Model control panel if you don't want it cluttering up your screen.

What you can do with a model display

Now that you have a model, what kinds of things can you do with it in the Visualizer module of Cerius²? (The Visualizer module is the one you've been using. It includes the controls that are accessed from the Visualizer main panel's menu bar and toolbar, as well as those on the left side of the Visualizer main panel. The stack of cards on the right side of the Visualizer main panel gives access to other modules.)

Note

14.   Labeling a model

Find the label popup on the toolbar.

The label popup is this one:

Set the label popup to ELEMENTS.

That is, click the label popup, drag down the list that appears, and choose ELEMENTS.

You can try using the label popup to replace the elements labels with labels that reflect other atomic properties. However, you have not defined some values (such as FFTYPE and CHARGES) and these labels display as question marks or zeros.

You can turn off labeling by setting the label popup to NO LABEL.

15.   Moving a model

You can rotate and translate your model in 3D space. You can do this by controlling the cursor with your mouse:

With the cursor near the middle of the model window, hold down the right mouse button and move the cursor vertically and then horizontally.

The model is rotated around the x- and y-axes, respectively.

Keyboard shortcut

If you have an extended keyboard, you can rotate about the x- and y-axes in large increments by using the left, right, up, and down arrow keys while the cursor is in the model window.

Now place the cursor close to an edge of the model window and move it parallel to that edge.

The model is rotated around the z-axis.

Hold down the middle mouse button and move the cursor around in the model window.

The model is translated in the x,y-plane.

16.   Zooming in or out on a model

You can control the magnification of the view of your model:

With the cursor in the model window, hold down the middle and right mouse buttons. Moving the cursor up and/or to the right increases the magnification. Moving the cursor down and/or to the left decreases the magnification.

Keyboard shortcut

If you have an extended keyboard, pressing the + and - keys on the keypad increases and decreases the magnification.

17.   Returning the model to the center of the model window

Click the reset tool on the toolbar to reset your model to its initial position.

The reset tool looks like:

Keyboard shortcut

<Home> on an extended keyboard also resets the view.

18.   Selecting atoms

Definition

Sometimes you will need to perform activities on only certain atoms, not on the entire model. For this purpose, you select atoms. You can select them one at a time:

Click any atom to select it.

A beep confirms that you've succeeded, and the atom is highlighted to indicate that it is selected.

Click another atom to select only it. Hold down <Shift> and click one or more atoms to select additional atoms. <Shift>-click an already selected atom to deselect it. Click any one atom to select it and deselect all others.

Or you can select several atoms at once:

Hold down the left mouse button and drag out a rectangle in the model window, so as to enclose several atoms. Drag out another rectangle to select a different group of atoms (or one atom). <Shift>-drag to select an additional group of atoms. <Shift>-drag some already selected atoms to deselect them.

You can select or deselect all atoms at once:

Click the selection tool to select all atoms. Click the deselection tool to deselect all atoms. Click empty space to deselect all atoms.

19.   Measuring components of the model's geometry

Select the Geometry/Measurements... menu item.

The Measurements control panel appears.

Click the Distance tool in the Measurements control panel.

The Distance tool looks like:

Click any two atoms.

A dashed line and a distance (in angstroms) are displayed on the model.

Most tools on Measurements control panel work similarly: click the tool, then click the required number of atoms. If you need more information, look ahead to Step 20.

Clear the measurements:

Click the DELETE Measurements action button.

Definition

Even though this button is small, it is an action button, as indicated by its blue color.

20.   Accessing on-screen help

To obtain help about any control in the Cerius² interface:

Move the cursor to a control about which you want information and click the right mouse button.

A help panel appears in the center of your screen.

Right-click any other control to replace the help with help about that control. Right-click a blank area of a control panel to obtain general information about the entire control panel. Click (left or right mouse button) the help window to make the help window disappear or click (left mouse button) any control panel to make the help window disappear.

Caution

21.   Changing the display style

Find the display style popup on the toolbar.

The display style popup is this one:

Set the display style popup to BALL.

Try setting the display style to BALL & STICK and CYLINDER. (ELLIPSOID, POLYHEDRA, and TRACE are irrelevant to your current caffeine model.)

You can display different parts of the model in different styles by selecting atom(s) before applying a style.

22.   Changing atom colors

Select the Build/Element Defaults menu item.

The Edit Elements control panel appears.

Enter C in the Current Element text entry box. Change the Display Color popup to some color other than dark grey.

You can change the default colors for other elements in a similar way,

23.   Coloring atoms according to a property

The functionality covered in this (optional) step is actually rather advanced, but it is new with release 3.0 of Cerius², so users interested in new features may find it useful.

Select the View/Colors... menu item.

The Color Selected Objects control panel appears. If we had defined a property such as charge or moveability, we could select all the atoms in the model and then simply click one of the items in the Color by a Property list to color the atoms. However, we haven't. So we will define our own property color map:

Click the Edit Mappings... pushbutton in the Color Selected Objects control panel to access the Edit Color Mappings control panel.

The Edit Color Mappings control panel appears.

Enter the name Mass in the New Map entry box, choose Mass from the Attribute popup, and set the Type popup to CONTINUOUS. Set the Minimum and Maximum Attribute Values betweenwhich the color range is to extend to 0.5 and 15.5, respectively. Check the Use Range check box and choose PEN_COLORS from the Use Range popup.

You can label atoms with their mass if you want. The atomic masses range from 1.01 (H) to 16.00 (O).

We use 0.5 and 15.5 rather than 1 and 15 so that divisions between colors occur between the atomic weights of atoms in our model. In addition, we use 15.5 rather than 16.5 because the PEN_COLORS color range contains 15 useable color entries, as we can see by displaying the color range:

Check the Show Range check box.

A color range appears on the right side of the model window. The first entry (zero) is invisible, since it is black and so is the window background.

Set the the Minimum and Maximum range-color entry numbers (in the Color Scheme section of the control panel) to 1 and 15, respectively. Select all atoms. Then, go to the Color Selected Objects control panel and choose Mass from the Color by a Property list.

All atoms except the oxygens are colored according to their atomic mass. We can color the oxygens by treating masses above 15.5 as outliers:

In the Edit Color Mappings control panel, click the Outliers... pushbutton next to the Max entry box to access the Maximum Outlier Handling control panel. Check the Pin to Maximum check box.

Oxygen is colored according to the maximum color entry number, 15.

Check the Use Pen check box and choose a color from the Use Pen popup.

Oxygen is colored with your chosen color.

You can experiment with some of the other controls in this control panel.

24.   Cleaning up the display or interrupting this tutorial (optional)

Close the open control panels if you have too many cluttering up your screen.

Use the File/New Session menu item to set all controls to their defaults and remove the model from the model window.

Reload your caffeine model. Or, if you want to stop for a while, please see Step 13 for exiting Cerius² and restarting this tutorial.

Building another model--ferrocene

25.   Adding a new model space

You already have a caffeine model, but we want to make an additional, separate model, ferrocene. To do this, we first make a "space" to contain the new model:

To open an additional model space, click the + tool just above the model table (which is the bottom-left part of the Visualizer main panel).

A new, empty model space becomes current, and the caffeine model is hidden.

26.   Sketching an iron atom

Ferrocene can be built much faster than caffeine:

Use the Build/3D-Sketcher... menu item to open the Sketcher control panel.

Iron isn't listed in the Sketch with popup; you can get it by using the periodic table.

Click the periodic table tool that's to the right of the Sketch with tool.

In other words, this control:

Click Fe in the Periodic Table window.

The Sketch with entry box is filled in with Fe. (Actually, you could have just entered Fe in the Sketch with entry box by typing, but we wanted to show you the periodic table.)

Click once somewhere near the center of the model window.

The single Fe atom is represented as a cross.

If you prefer the Fe to be represented as a ball, select the View/Display Attributes... menu item. Then, in the Display Attributes control panel, click the Preferences... button. In the Style Preferences control panel, set Lone Atom Style to BALL.

27.   Adding the ligands

Click the Templates... button in the Sketcher control panel. In the Sketcher Template control panel, double-click ligands/ and then double-click pentadienyl.

(You may have to move up out of the organic directory, if you haven't restarted Cerius² since the beginning of this tutorial.)

The template tool is now selected and allows you to add pentadienyl ligands to the iron.

Click the Fe atom.

This adds one ligand.

Click the Fe atom again. Select the selection tool in the Sketcher control panel, and move the model so that the rings appear to be nearly superimposed.

You'll notice that the ferrocene model is not symmetrical and that pressing the CLEAN button does not make it exactly symmetrical.

If you have purchased one of the QUANTUM 1 applications (ADF, DMol³, GAUSSIAN, MOPAC, or Zindo), you may use their symmetry function to fully symmetrize the model:

Click the popup above the deck of cards (it should be labeled BUILDERS 1) on the right side of the Visualizer main panel and choose QUANTUM 1. The menu card for any of these quantum chemistry applications contains a Geometry/Symmetry menu item. Select it to access a Symmetry control panel. Change the Tolerance popup to COARSE. Click the Find symmetry action button.

Reading in additional models

Click the File/Load Model... menu item to access the Load Model control panel. In the control panel, double-click Cerius2-Models and then double-click one of the subdirectory names. If you obtain another list of subdirectories, double-click the desired one. Double-click the name of any model you think might be interesting.

A third model space is created, displaying the chosen model. Both the caffeine and ferrocene (named Model2) model spaces are hidden.

Locate the model table in the lower left of the Visualizer main panel. In the list of model names, click Model2 and type ferrocene, then press <Enter>.

You may save the ferrocene model if you want.

Use the Load Model control panel to load a few (2-4) more models. If you want a model from a different subdirectory, you can double-click ../ to go up one directory level or use the popup above the files list box to go directly to any parent directory.

Managing multiple models

Notice the column of diamonds in the model table.

That is, these items:

The diamond that is highlighted in red and looks 3-dimensional indicates the name of the current model.

Definition

In the above example, glycine is the active model. It is both current (activities done in control panels or with the mouse affect it) and the only model visible in the model window.

30.   Viewing a hidden model

Say you'd rather look at ferrocene than the currently active model:

Click the empty diamond next to the ferrocene model name.

That diamond becomes highlighted and ferrocene replaces the other model in the model window.

You may make other individual models current by clicking their diamonds.

31.   Viewing several different models simultaneously

Notice the column of squares in the model table.

That is, these items:

The square that is highlighted in cyan and looks somewhat 3-dimensional indicates the visible model. Click one of the empty squares.

The model window becomes divided into one large square display area and a border of smaller square display areas. The current model (ferrocene, if you performed only the boxed instruction in Step 30) is in the largest square display area. The model you just specified is displayed in one of the smaller square display areas.

Click one or more additional empty squares in the model table.

Each model is displayed in one of the smaller square display areas.

Click a square that's already highlighted in blue.

That model now becomes hidden.

Notice the display mode tools.

That is, these tools:

The border mode tool is currently active.

Select the grid mode tool (directly above the currently selected border mode tool).

The display is divided into 4 or 9 (or 16, etc., depending on how many visible models you have) equal-sized display areas. The current model is displayed in the lower-left corner of the model window.

Select the overlay mode tool (the topmost one of these three tools).

All visible models appear in the same display area.

Click the border mode tool again, so that the current model appears in a large square display area, with the others in smaller square display areas.

32.   Adding and deleting model spaces

You've already learned (in Step 25) how to add a new, empty model space by clicking the + tool. You can also clear an existing model space (i.e., remove the model, leaving its model space empty) or delete a model space (i.e., remove both the model and its space from the current Cerius² session):

To delete a model space, click a diamond to make the desired model current, then click the - tool . Click OK in the confirmation window that appears.

The number of models listed in the table decreases by one (the remaining models are not renumbered).

To clear a model space, click a diamond to make the desired model current, then click the clear tool . Click OK in the confirmation window that appears.

The model space and the current display area are cleared, but the model name and number remain in the model table. You may sketch a new model in this display area (and model space). You may also copy one of the other models into the cleared space (if you, say, wanted to make an analog of caffeine):

33.   Copying models from one model space to another

Leave the cleared model space defined as current (the largest display area is empty). Click in an empty part of one of the other display areas, continue holding down the mouse button, and drag the cursor into the current (empty) display area.

In other words.

The copied model now exists as two separate models in two separate model spaces.

To avoid confusion, you should rename the current model space so that the name reflects the model that's currently occupying that space (or the name of the analog or complex that you intend to construct from the newly copied model).

For example, click the name of the current model in the model table and change it to caffeine analog.

You can also copy a model into a currently occupied model space, if, say, you want to join them together into a complex or new model:

Click in an empty part of one of the other display areas and drag the cursor into the current (occupied) display area.

The models will be on top of one another, but you can move them apart as follows:

Go to the right atom selection popup on the toolbar of the Visualizer main panel. Click and drag to change it from Atom to Frag. Click an atom in one of the fragments in the current model space. Holding down <Ctrl> and the middle-mouse button, drag that fragment away from the other. Make sure both atom selection popups are set to Atom when you are finished.

34.   Cleaning up the display or interrupting this tutorial (optional)

Close the open control panels if you have too many control panels cluttering up your screen.

Use the File/New Session menu item to set all controls to their defaults and remove the models from the model window.

Reload your caffeine model. Or, if you want to stop for a while, please see Step 13 for exiting Cerius² and restarting this tutorial.

Printing a model

If you've deleted caffeine from your Cerius² session, please reload it (see Step 13 if you need instructions). You may have to use the file browser in the Load Model control panel to navigate back up to the directory in which you stored caffeine.msi.

If several models are visible, make caffeine the only visible (and active) model by assuring that the visibility controls (square blue icons in the model table) are toggled off for all other models and on (highlighted) for caffeine.

Change the display style from STICK to something else if you prefer (see Step 21).

Select the File/Print... menu item. In the Print control panel, change the Command to the statement that you usually use to specify printing to a postscript printer.

An experienced user at your site, or your systems administrator, should know this command if you don't.

Either select the PRINT button or change the settings of some of the other controls and then select the PRINT button.

If nothing happens

Controlling the 3D display

Depth cueing gives an impression of 3-dimensionality by causing the atoms that appear to be closest to the viewer (you) to appear brighter, and those farther away, to fade into the background. You may want to adjust or turn off this feature.

Select the View/Graphics menu item.

When you drag the cursor down to the Graphics item, a pullright menu appears.

Continue dragging the cursor (to the right and then down) and release the mouse button over the View/Graphics/Depth Cueing... menu item. In the Depth Cueing control panel, click the control on the Depth Cue Factor slider and drag it to the right.

The Depth Cue Factor slider and entry box now look like:

You can also change the depth cue factor by entering a number in the Depth Cue Factor entry box.

A depth cue factor of 1 turns depth cueing off. Setting it to zero results in extreme depth cueing (the atoms farthest away from you will probably appear black).

Now set the Depth Cue Factor to some value less than 1.0.

When the depth cue factor set to some value less than 1, you can use the Far Distance and Near Distance sliders to adjust the points at which depth cueing takes effect. The adjustments take effect immediately and are more easily seen at lower values of the depth cue factor. Since caffeine is a nearly planar model, you can see the effects of depth cueing more readily by turning it so that it is no longer parallel to the computer screen.

36.   Lighting your model

Lighting effects are more dramatic if you have a model with some solidity, so:

Change the display style to BALL. Select the View/Graphics/Lighting... menu item.

The Lighting control panel appears. You can experiment with the controls on and accessible from this panel. Remember, you can click with the right mouse button to obtain help on any control.

You can, for example:

• Change the color of the global ambient light by adjusting the Color sliders in the Lighting control panel. Make it a rather dim, neutral color, so that you can more easily see the effects as you add light sources (More lights). You can even turn it off by setting Gray to 0.0.

• Click the Color... button to access the Lightsource Colors control panel, where you can change the colors and brightness of the various components of LIGHT 1.

If nothing happens

Click the Position... button in the Lighting control panel to access the Lightsource Position control panel, where you can change the light from directional to positional and then change its position. For example, set the X, Y, and Z values to 1, -1, and 10, respectively, to place a light in front of the model, somewhat to its lower right.

Click the Spotlight... button in the lighting control panel to access the Spotlight Settings control panel, where you have additional control over the positions of spotlights (positional light sources).

For example, set the Latitude and Longitude controls on this control panel to 5.68 and 174.29, respectively, to shine the light back towards the model. Narrow the Cutoff to, say, 20° to make a narrow beam of light. Try increasing the Falloff value to smooth the transition from the light to the dark area.

Iteratively change the Position controls in the Lightsource Position control panel and the Direction controls in the Spotlight Settings control panel so as to, for example, illuminate a particular atom or center the light on the 6-membered ring.

Click the Attenuation... button in the Lighting control panel to access the Lightsource Attenuation control panel. Try increasing the Linear or Quadratic factor to make atoms farther from the lightsource appear dimmer. The effect is more apparent if the illuminated part of the model is nearly parallel to the direction of the light beam.

• Add a second light source by changing the Light popup in the Lighting control panel to LIGHT 2 and checking (i.e., clicking, so that a checkmark appears in the check box) the Enabled check box.

Use the Lightsource Colors control panel to change the color of LIGHT 2. Make it different from LIGHT 1 so you can more easily see what's happening as you adjust the lights.

Select the Utilities/Customize/Pen Colors... menu item. In the Pen Colors control panel, set the Background popup to OTHER or set the Pen popup to BACKGROUND. Use the color sliders to customize your background's color.

Or just set the Background popup to one of the predefined color choices.

Exploring Cerius2 on your own

Select the Help/Getting Started... menu item.

You can use the buttons in the Getting Started control panel to find out more about:

• The names of the parts of Cerius²'s graphical environment and how to manage all the windows.

• Loading models.

• Manipulating models in the model window, including:

Access to on-screen summaries of mouse- and keyboard-actions for selecting and moving models.

Information on changing the display style and atom colors, as well as on labeling atoms.

• Building models (icons in some of these help panels function just as they do in the Sketcher control panel).

• Performing simple and complex selections and simple editing of your selections.

The Example files control panel allows you to load and automatically play back some pre-recoreded examples of many things that can be done with Cerius². Most of these examples use other modules, in addition to the basic Visualizer controls. Try some of them! (You must, of course, have licensed copies of any programs used in these tutorials.)

Select the Help/About Cerius2... menu item.

The About Cerius2 control panel contains information on contacting Molecular Simulations, Inc. It includes our website's URL and the email and other addresses for obtaining customer support.

39.   Experimenting with other features of the interface

Now that you've gained some familiarity with Cerius², you can explore more of its features on your own. You cannot cause any permanent damage:

• Unless you specifically save, for example, changes you make via the Utilities/Customize menu items, Cerius² will revert to all its default settings the next time you start it.

• You can use the File/New Session menu item to, in effect, restart Cerius² without actually quitting and reloading it.

• Many module cards have a Reset function, which returns control settings to their defaults.

Detailed information on all the functions of the Visualizer are found in the other sections of this documentation set.

Tables of the mouse and keyboard functions can be found under Mouse and Keyboard Actions.

Detailed information about modules other than the Visualizer are found in the documentation for the applications to which those modules belong.

41.   Quitting your Cerius² session

Select the File/Exit menu option. Click Exit in the confirmation window that appears.

Summary--Some of what you've learned

• Using and managing menus, windows, and other controls in the Cerius² interface (e.g., Locating the basic building tool, Cleaning up your screen, see also The Cerius2 Interface).

• Building models (see Building a model--caffeine, Building another model--ferrocene, see also Building Models).

• Sketching with templates and ligands (see Sketching the ring system of caffeine, Here's another way of adding a methyl group:, Adding the ligands, see also Adding templates (groups of atoms)).

• Changing atom elements and bond types (see The Edit Element tool looks like:, Correcting the bond order, see also Changing atoms and their bonding types).

• Using the periodic table (see Sketching an iron atom).

• Adding the correct number of hydrogens (see Correcting the hydrogens, see also Adding hydrogens).

• Cleaning up the conformation (see Cleaning up the conformation, see also Refining the conformation).

• Using file browsers to find models and templates (see Stop when you see the filename methyl., Reading in more models, see also Managing Models and Sessions).

• Saving and loading models (see Saving your caffeine model, Reading in more models, see also Managing Models and Sessions).

• Labeling a model (see Labeling a model, see also Labeling and annotating models).

• Moving a model (see Moving a model, Zooming in or out on a model, Returning the model to the center of the model window, see also Moving models on the screen).

• Changing a model's display style (see Changing the display style, see also Model display style).

• Selecting atoms and groups of atoms (see Selecting atoms, see also Selecting atoms and groups of atoms).

• Measuring parts of a model (see Measuring components of the model's geometry, see also Geometry Analysis).

• Managing multiple models (see Adding a new model space, Reading in more models, Managing multiple models, see also Handling multiple models).

• Coloring a model according to atomic properties and creating property maps (see Coloring atoms according to a property, see alse Coloring atoms by properties, Property-color mapping).

• Manipulating lighting and colors (see Changing atom colors, Controlling the 3D display, see also Enhancing Model Display).

• Printing a model (see Printing a model, see also Printing models and graphs).

• Accessing on-screen help (see Accessing on-screen help, Using the Help menu, see also On-screen help).