Cerius2 Modeling Environment

5       Building Models

The Cerius²·Visualizer provides a variety of tools for making new models and changing existing models. These include a mouse-driven 3D-Sketcher for constructing and editing models (this section), as well as features that enable you to position atoms precisely (Precise positioning of atoms during building), edit the properties of selected atoms or elements (Editing element and bond attributes), change bonding (Changing the hybridization and adjusting the valence), and introduce disorder (Introducing substitutional disorder). You can also annotate the model by adding items such as text, arrows, and boxes (Viewing and Displaying Models).

These general-purpose basic and advanced building and editing tools are directly available from the Build, Edit, and Move pulldown menus on the main control panel's menu bar.

Other builders designed for constructing more specialized models are available as separate modules and are accessed with the deck of cards menu. They have separate documentation.

This section explains

Basic building

Selecting atoms and groups of atoms

Basic editing

Advanced building and editing

Other builders

Basic building

This section tells you where to access the basic building tools and how to perform tasks that are typically associated with building the basic skeleton of a small model. It contains information on:

Starting to construct a new model

Adding atoms and bonds

Adding templates (groups of atoms)

Fusing and connecting fragments

Adding hydrogens

Related information

Basic editing tasks, including changing element types, bonding, and model conformation, are presented under Basic editing. The final task you would perform for building almost any model would be to optimize its configuration (Refining the conformation). Storing models in files is presented under Saving model structure files.

Selecting atoms is presented under Selecting atoms and groups of atoms.

Tasks that may be less often or less typically performed, such as editing atom attributes and changing defaults and preferences, are covered in Advanced building and editing.

You should already know...

If you have never used Cerius² before or are unfamiliar with the terminology used to indicate how to use its interface, please go through the model-building example in Introducing Cerius2 before continuing with this section. How to start Cerius², the names of parts of its interface, as well as basic mouse usage and how to access on-screen help, are covered in The Cerius2 Interface,

Starting to construct a new model

You can probably construct a model of almost any small model you want, simply by straightforward trial-and-error use of the 3D-Sketcher. This procedure will probably be good enough if you have to build only a few models. However, Cerius² building tools typically offer several ways of accomplishing the same end.

Therefore, depending on the types and number of similar models you need to work with, a more considered approach (including the use of model-building or -generating tools other than those contained within the Visualizer and not documented here) may prove more efficient. So, it should be helpful for you to obtain some familiarity with all the relevant tools as you develop your own model-building style, using whatever combination of tools and order of tasks that works best for your purposes.

Task-oriented information

This section presents information in a task-oriented way, generally presenting simpler or default methods first. The organization assumes you would build the complete skeleton of a structure first and then edit it as desired. However, the task orientation (rather than tool orientation), as well as ample use of headings and labels, should facilitate your finding information, no matter what approach you use.

Note

Some possible approaches

A few of many possible approaches include:

• Build a model using carbon atoms and available templates, then edit the element and bond types as desired.

• Add hydrogens as the heavy-atom skeleton is being built or after it is complete.

• Keep the conformation and topology as correct as possible while building a model or build a distorted model and then adjust its conformation and/or connectivity.

• Add several identical templates simultaneously at several points of a base model, then edit the individual functional groups as needed.

• Build a small model, copy it, edit both copies as desired, and then join the fragments into one larger fragment.

• Build small fragments, then use them as the basis for constructing larger models or as starting structures for use with the more specialized builders available as other Cerius² modules.

• Load templates from disk, then edit, fuse, and/or connect them to form a larger fragment.

• Load or generate a periodic system (Other builders), then edit it.

How it works

Clicking any of the icon tools on the Sketcher control panel alters the function of the left mouse button. Selection mode, when the selection tool (the arrow in the upper left of the Sketcher control panel) is highlighted, is the default for cursor behavior. Clicking other icon-type tools enables you to use the cursor, for example, to place atoms, manipulate angles, or change an atom's element type.

Many of the functions can be performed on several atoms simultaneously. This is done by first selecting (Selecting atoms and groups of atoms) the atoms, then double-clicking the appropriate tool. (If the tool is already active, only one click is needed to perform the action.)

In some Sketcher modes, a property of the structure can be changed by moving the mouse in the model window. Generally, dragging left-to-right or bottom-to-top while holding down the left mouse button increases a value (e.g., a bond length), and dragging in the opposite direction decreases the value.

Recovering from mistakes

An UNDO button, 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 it is not usable.

Help

Checking the Guide? check box gives you on-screen help (in the upper left corner of the model window) on the 3D-Sketcher.

Examples

Detailed examples of using the Sketcher control panel to build caffeine (Building a model--caffeine) and ferrocene (Building another model--ferrocene) are included in this guide.

Other basic building tools

Most of these enable better control over exactly how the controls operate than does the 3D-Sketcher control panel and may therefore enable faster building under certain circumstances.

These alternatives to the sketcher often provide full support of periodic models in areas where the Sketcher does not (for example, to add atoms to a periodic system, you have to use the Add Atom control panel rather than the 3D-Sketcher control panel).

Some items in the Edit menu may provide quicker action than equivalent tools in the Sketcher control panel (especially if the Sketcher control panel is not open and you need to make only a few changes).

Adding atoms and bonds

Note

Selecting the element type

You can change the sketching element type, if needed, in any of several ways:

• Click this entry box and enter an element name in it.

• Choose an element from the popup immediately to the right of this text entry box. This popup lists several commonly used elements.

• Select the periodic table tool to the far right of this text entry box. When the Periodic Table window appears, select the desired element.

Adding atoms and single bonds

To begin sketching, simply click the Sketch with tool to activate it (if it is not already active--when an icon-type tool is active, it is colored dark purple.) When you move the cursor into the model window, it is shaped like a triangle, indicating that you are in sketch mode, that is, that clicking the left mouse button places an atom and/or bond rather than selecting an atom (or some other activity). The element that is used in sketching is specified as described under Selecting the element type.

You can use the Sketch with tool to start building a new model and to add atoms to existing models.

Placing the first atom

Click anywhere in the model window to place the first atom. Move the cursor away--a dashed line follows the cursor, connecting it with the atom you clicked and indicating where the bond to your next atom will lie.

Tip

What next?

After placing the first atom or when adding to an existing model, you can use the sketch mode for several tasks:

• To place a second atom, click where you want it to appear. Continue clicking to place subsequent atoms in a chain.

• To end a chain, double-click when you place the last atom, click again on the last atom added, or move the cursor outside the model window. The dashed line no longer appears.

Tip

• To close a ring or connect a chain to an existing ring or chain, click the appropriate existing atom.

• To place a bond between two atoms that are not bonded to each other, click each atom. (You can also use the Connect tool or the Edit Bond tool for this purpose--see Connecting fragments and Changing the bond type.)

• To start a new chain or ring, end the first one (see above) and then click in empty space.

• To add a branch to an existing chain or ring, click the atom that is to be the branch point, then click in empty space.

• To sketch with a different element type, select a different element type (Selecting the element type), then click the atom in the model window to which you want to add the new element.

Tip

Other sketch-mode functionality

While in sketch mode, you can also:

• Change the type of bond from single to double (or from double to triple) by clicking the atoms at each end of the bond.

When you use the 3D-Sketcher, you manually place atoms in the model window, then refine the atom positions later (see Refining the conformation). Another builder tool, the Add Atom control panel, enables you to add atoms to the current model one at a time at specified coordinate positions. You can use it to build models and to add to existing models. Although less convenient to use than the Sketcher control panel, the Add Atom control panel allows precise control over the positions of atoms, which is particularly useful for duplicating published crystal structures or inorganic structures.

To access the Add Atom control panel, select the Build/Add Atom... menu item from the main control panel.

Set the element type by entering the desired element name in the Element entry box or by accessing the Periodic Table window from the Add Atom control panel.

Specify the coordinate system to be used for positioning atoms by choosing from a popup: Cartesian coordinates (XYZ), crystal fractional coordinates (ABC), or surface fractional coordinates (UVd) for nonperiodic, 3D periodic, or 2D periodic systems. Then click the associated entry box and enter the exact coordinates at which to place the atom.

Other properties

Several other atom properties can optionally be specified before placing an atom in the model window: hybridization, charge, occupancy, the atom name, and temperature factors (Specifying temperature factors)--see the on-screen help for details. Hybridization is also discussed under Changing the hybridization and adjusting the valence--the hybridization popup in the Add Atom control panel functions the same as in the Sketcher control panel.

Placing the atom

After setting all desired parameters, click the ADD ATOM action button to place the atom in the model window. The most recently added atom can be deleted by clicking the UNDO button.

Adding templates (groups of atoms)

Note

Selecting templates

To use a different template, click the Templates... pushbutton to the right of the template tool. This 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 that contain templates.

Using the file browser to navigate the directory structure is fairly intuitive. The procedure is described under Loading model structure files.

Example

A specific example of using the file browser to find and load a template is demonstrated under The Templates... button looks like:.

Loading a template

Once you find the desired template file, load it by:

• Selecting its name and then clicking the LOAD button.

or:

• Double-clicking its name.

Adding templates to a model

Once the desired template is chosen (see Selecting templates), click the template tool to activate it, if it is not already active. The cursor is now shaped like a T when it is over the model window. You can use the template to start building a model or to add a group to an existing model:

• To add the template as a separate (or new) fragment, click in empty space.

• To add the template at an existing atom, pick that atom. It is attached in a reasonable way (e.g., by replacing a hydrogen).

• To add identical templates simultaneously to several atoms, first select the atoms (Selecting atoms and groups of atoms), and then double-click the template tool (or single-click if it is already active). Hydrogen atoms are replaced as appropriate.

To save a template if you don't have the Analog Builder, follow these steps:

1.   Construct the template model, making sure you are satisfied with its final structure and conformation (this section).

2.   Decide which hydrogen atom should be the point at which the template is to be added to other models.

3.   Replace this hydrogen with a dummy element of type X (Changing the element type).

4.   Save the model in .msi format (Saving model structure files).

Fusing and connecting fragments

Fusing fragments

Fusing two fragments (in the model window) means to join them so as to delete a heavy (non-hydrogen) atom. For example, two benzenes could be fused to form naphthalene, or many cyclohexanes and cyclopentanes could be fused in building buckminsterfullerene.

The Fuse tool on the Sketcher control panel can be used in several ways:

• To fuse two fragments at one point, select the Fuse tool, then pick an atom in each fragment. Click the second atom again to perform the fusion. The first atom picked is deleted, and the rest of the fragment is bonded to the second atom.

• To fuse several atom pairs simultaneously:

Select the Fuse tool and pick each pair in succession. Then click the last atom a second time.

or:

While in selection mode, select all the atom pairs to be fused (Selecting atoms and groups of atoms), then double-click the Fuse tool.

Connecting two fragments means to join them by a bond (deleting only hydrogens as necessary). For example, two benzenes could be connected to form biphenyl or connected twice to form biphenylene.

The Connect tool on the Sketcher control panel can be used in several ways:

• To connect two fragments by a single bond, select the Connect tool, then pick each of the two atoms to be connected by a bond. The fragments become oriented so as to give a reasonable bond length and orientation, and extra hydrogens are deleted as appropriate.

• To place a bond between two atoms in the same model, select the Connect tool, then pick each of the two atoms.

Tip

Adding hydrogens

Note

You may add hydrogens to your model at any time and in several ways.

• Wait until you have finished building and editing your structure, then click the H ADJUST button. Hydrogens are added to or deleted from all atoms (as needed) in the current model so that their valences are satisfied.

• Select the Hydrogen tool and then pick atoms whose valences you want to satisfy by adding or deleting hydrogens. Alternatively, select these atoms first (Selecting atoms and groups of atoms), then double-click the Hydrogen tool.

• Check the Draw with Hydrogens check box. Hydrogens are automatically added to or deleted from atoms as you sketch your model.

• Use the Sketch with tool with the Sketch with entry box set to H (Adding atoms and bonds).

• Use the Add Atom control panel (Precise positioning of atoms during building) if you need to control hydrogen positions exactly.

• Change selected atoms to H, using editing tools (Changing the element type).

• To delete all hydrogens, select hydrogens by element (Selecting and deselecting individual atoms), then use the Delete Atom tool in the Sketcher control panel or the Edit/Delete menu item in the main control panel (Deleting atoms and bonds).

If any of the automatic tools give the wrong number of hydrogens at some atom(s), you can change their hybridization state (Changing the hybridization and adjusting the valence), formal charge (Changing the formal charge), and/or the bond type between that atom and another heavy atom (Changing the bond type) and then adjust the hydrogens again.

Selecting atoms and groups of atoms

You need to select one or more atoms when you want to perform some function (e.g., editing, labeling, changing the display style) on only certain atoms.

You can select atoms individually or according to some criterion, such as a common property or their membership in a group. Selection criteria may be quite complex.

This section contains information on:

Selecting and deselecting individual atoms

Selecting atoms in several models

Selecting and deselecting collections of atoms

Customized atom selection

The controls

The Edit pulldown menu and the toolbar in the Visualizer's main control panel offer several ways of selecting one or more atoms. There are also four atom selection tools in the toolbar:

Example

Several ways of selecting individual atoms are demonstrated under Selecting atoms.

Related information

You can also select atoms in several models simultaneously (Selecting atoms in several models).

Selecting and deselecting individual atoms

The mouse is in selection mode when the selection tool in the Sketcher control panel is highlighted. (In addition, the cursor is shaped like an arrow pointing to the upper left when it is in the model window.) This tool is also found in other control panels, and selection is always the default mode.

You always use the left mouse button to select atoms in the model window.

Single-atom picking

• To select only one atom, simply click it. A beep confirms that you've succeeded, and the atom becomes highlighted.

• To select only one different atom, click it.

• To select additional atoms, keep <Shift> depressed and click the appropriate atoms (in other words, <Shift>-click them).

• To deselect some (but not all) selected atoms, <Shift>-click them.

• To select only all atoms in some area of the model window, click nearby and drag out a selection rectangle that encloses the desired atoms. (The atoms must be visible to be selected; see Visibility of polymer backbones.)

• To add all atoms in another area of the model window to the selection, <Shift>-drag a selection rectangle around them.

• To deselect a group of already-selected atoms, <Shift>-drag a selection rectangle around them.

• To select all atoms, drag out a rectangle enclosing the entire model, select the Edit/Select All menu item, press <Alt> a on the keyboard, or click the select all tool (see toolbar illustration at The controls).

Tip

• To deselect all atoms, click in empty space (in the model window) or click the deselect all tool in the toolbar.

You should already know...

Managing and displaying multiple models is documented in Managing Models and Sessions.

How it works

Selecting atoms works differently, depending on how the models are displayed (see Controlling model visibility and the display mode):

• In overlay mode, all the single-atom picking and selection-rectangle methods listed above (Single-atom picking) can be used to select atoms in all displayed models.

• In border mode, all the single-atom picking methods listed above (Single-atom picking) can be used to select atoms in all displayed models. The selection-rectangle methods function only for the current model (see Specifying the current model).

• In grid mode, all the single-atom picking methods listed above (Single-atom picking) can be used to select atoms in all displayed models.

A single pick in the model window (by the same selection process as described under Selecting and deselecting individual atoms) can act on different pick targets. A single click can pick a single atom, all atoms in one residue, all atoms in one chain, or all atoms in one model. Similarly, using a selection rectangle can pick only the atoms within the rectangle, or all residues, chains, or models that have at least one atom within the rectangle.

To change the default behavior (i.e., picking individual atoms), change the pick target popup on the toolbar (see The controls) from Atom to Residue, Chain, or Model. Residues and chains are not present in all models, but may be defined in other Cerius² modules, which are documented separately.

What is selected

When you pick a target, other items (in addition to the target) might also be selected, depending on your selection criteria.

Selection can apply to only the single atoms actually picked; or to all atoms with the same name, same element type, or same forcefield type; or to all of a bonded set of atoms (a fragment) or of the smallest set of bonded atoms leading away from the main model and starting after the selected atom ("short end").

To change the default behavior (i.e., picking individual or contiguous atoms), change the select-what popup on the toolbar (see The controls) from Atom to Name, Element, FF (forcefield type), Fragment, or End (short end). Names atoms are not present in all models, but may be defined in other Cerius² modules, which are documented separately. You can also name atoms with the Edit Selected Atoms control panel (Atom properties).

Depending on the setting of the pick target popup, you can also select all residues of the same Type or Identifier or all chains of the same Name. The default is to select all atoms in a residue, chain, or model.

Selection is within...

In addition to the selection criteria, you can restrict or expand the selection scope; for example, whether atoms are selected in the current model or all models, etc. To change the default selection scope (i.e., within the current model, use the Atom Selection control panel (see Additional selection criteria).

How it works

Not all combinations of pick target, selection criterion, and selection scope make sense or are allowed. The supported combinations are shown in Table 2.

Table 2. Possible combinations of pick target, selection criterion, and selection scope

pick target	what is selected	selection can be within...
atom1	The atom(s) actually picked11	In one model.1 In all2 models (see Selecting atoms in several models).
atom1	All atoms of the same name. All atoms of the same element type. All atoms of the same forcefield type.	All in the same residue. All in the same chain. All in the same model.1 All in all2 models.
atom1	All atoms in the same fragment. Smallest set of bonded atoms.	In one model.1 In all2 models.
residue	All atoms in the residue(s) actually picked.1	In one model.1 In all2 models.
residue	All atoms in all residues of the same type. All atoms in all residues of the same ID.	All in the same chain. All in the same model.1 All in all2 models.
chain	All atoms in the chain(s) actually picked.1	In one model.1 In all2 models.
chain	All atoms in all chains of the same name.	All of this chain name in the same model.1 All of this chain name in all2 models.
model	All atoms in the model picked.1	All atoms in all2 models.

1 Default value. 2 Or in all visible models or in selected models.

Additional selection criteria

Select the Edit/Selection... menu item to access the Atom Selection control panel. This control panel enables you to specify the Pick target, Select atom(s) which are, and Within criteria when the mouse is used for selection (see Selecting according to properties).

In addition, more selection criteria are available. These functions are not linked to mouse activity in the model window, but occur when an icon or action button in the control panel is clicked.

For example, you can select all atoms within a specified radius of a selected atom, all atoms in a named group, or all backbone atoms in a polymer. See also Defining and selecting groups and Customized atom selection.

Additional information

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

Defining and selecting groups

You can define any collection of atoms as a "group" and then perform group-based selections.

To define and name such groups, access the Groups control panel by selecting the Edit/Groups... menu item. You can also rename, redefine, or delete the group definitions.

Selecting groups

You can select groups by clicking the Select objects action button in the Groups control panel or the Select Group button in the Atom Selection control panel.

Customized atom selection

Accessing the tools

Select the Edit/Selection... menu item to access the Atom Selection control panel. Click the Custom Selection... pushbutton to access the Customized Atom Selection control panel.

Setting multiple and customized criteria

To set up customized selection criteria, you can pick properties from the popups in the Customized Atom Selection control panel and enter additional subcriteria in the associated entry boxes.

Wildcards are allowed in the subcriteria. Also, multiple subcriteria may be entered into an entry box--separate the individual subcriteria with a colon (:).

For example, you can select all atoms whose name starts with c, which have a desired range of charge values, and are located within residues of a certain type.

For maximum flexibility, you can also use raw object reference language to select atoms. Please see the on-screen help for the syntax.

Finding atom information

To enter information into the subcriteria boxes, you of course need to know what an atom's properties are.

You can query atom properties by shift-clicking the atom with the right mouse button. This displays a temporary message box and also prints to the text window.

You can also choose to have brief information on atom properties sent to the text window whenever you click an atom. To do this, select the Utilities/Customize/Environment... menu item to access the Customize Environment control panel. Check the Echo object reference check box.

Additional information

Please see the on-screen help for the precise syntax for entering subcriteria and for details on the functioning of each control in the Customized Atom Selection control panel. The help that is accessed with the ? buttons on this control panel is context-sensitive; that is, what help is displayed depends on what the associated popups are set to. The cumulative criteria are displayed in the Object Reference entry box as they are built up with the other controls in this control panel. The context of the Object Reference entry box may be edited.

Basic editing

Most models require some editing after the basic skeleton is built or while the model is being built. You may also want to edit models that were read in from a file. This section tells you where to access the basic editing tools and how to perform tasks that are typically associated with editing a model. It contains information on:

Changing atoms and their bonding types

Editing the structure

Refining the conformation

Related information

Basic building tasks are presented under Basic building.

Tasks that may be less often or less typically performed, such as editing atom attributes and changing defaults and preferences, are covered in Advanced building and editing. Displaying labels and other information about atoms in a model is presented in Labels.

You should already know...

You need to know how to select atoms in your model (Selecting atoms and groups of atoms), so you can edit them. You also of course need to know how to build a model (Basic building) and/or load a model from a file (Loading model structure files).

You may want to review the basics of how the controls in the Sketcher control panel work (see How it works).

Note

Changing atoms and their bonding types

Changing the element type

Changing the formal charge

Changing the bond type

Changing the hybridization and adjusting the valence

To change the element type of an existing atom in the model window, you use the Edit Element tool.

Specifying the element type

The edit element type (i.e., the element that you want the atom to become) is listed in an entry box to the right of the Edit Element tool:

You can change the edit element type in any of several ways:

• Click this entry box and enter an element name in it.

• Choose an element from the popup immediately to the right of this text entry box. This popup lists several commonly used elements.

• Select the periodic table tool to the far right of this text entry box. When the Periodic Table window appears, select the desired element.

If the Periodic Table window is already open, click the periodic table tool to link it to the Edit Element function.

Tip

Changing the default element type automatically activates the Edit Element tool. If the edit element type is already correct, you can activate the Edit Element tool by clicking it.

Changing the element type

You can change atoms in the model window to the element type specified in the element type entry box in several ways:

• Select the Edit Element tool and then pick the desired atom(s).

• Select the desired atom(s) (Selecting atoms and groups of atoms) and then double-click the Edit Element tool.

If you want to edit both the element type and other properties simultaneously, select the Build/Edit Atoms... menu item. This gives access to the Edit Selected Atoms control panel.

Additional information

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

Changing the formal charge

To change the formal charge on an atom, use the Edit Formal Charge button in the Sketcher control panel.

Specifying the formal charge

Choose AUTO or the desired value of the formal charge from the popup to the right of the Edit Formal Charge tool.

Changing the default formal charge automatically activates the Edit Formal Charge tool. If the formal charge is already correct, you can activate the Edit Formal Charge tool by clicking it.

Changing the formal charge

You can change the formal charge on atoms in the model window to the value specified by the formal charge popup in several ways:

• Select the Edit Formal Charge tool and then pick the desired atom(s).

• Select the desired atom(s) (Selecting atoms and groups of atoms) and then double-click the Edit Formal Charge tool.

Tip

Changing the formal charge together with other properties

If you want to edit both the formal charge and other properties simultaneously, select the Build/Edit Atoms... menu item. This gives access to the Edit Selected Atoms control panel.

Additional information

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

Changing the bond type

To change the bond type between any two atoms, use the Edit Bond button in the Sketcher control panel.

Specifying the bond type

Choose SINGLE, DOUBLE, TRIPLE, or RESONANT from the popup to the right of the Edit Bond tool.

Changing the default bond type automatically activates the Edit Bond tool. If the bond type is already correct, you can activate the Edit Bond tool by clicking it.

Changing the bond type

You can change bonds in the model window to the type specified by the bond type popup in several ways:

• Select the Edit Bond tool and then pick two atoms. If a bond exists between the atoms it is changed to the type specified. If no bond exists, one (of the desired type) is created.

• Select the desired atom pair(s) (Selecting atoms and groups of atoms) and then double-click the Edit Bond tool. Existing bonds are changed to the type specified. No new bonds are created if more than two atoms are selected.

Tip

Additional controls over bonding

If you want to edit the bond type and also change how bonds are calculated (see Editing element and bond attributes), select the Build/Edit Bonds... menu item. This gives access to the Edit Connectivity and Bonding control panel.

Additional information

Please see the on-screen help for details on the functioning of each control in the Edit Connectivity and Bonding control panel. (Setting the bond calculation preferences is discussed under Bond properties.)

Changing the hybridization and adjusting the valence

To change the hybridization for any selected atom, use the Edit Hybrid tool.

Tip

Specifying the hybridization

Choose the desired type of hybridization from the popup to the right of the Edit Hybrid tool. AUTO means to allow Cerius² to automatically determine the hybridization; the specific types listed in the popup are self-explanatory; OTHER should be used for high-coordination centers not specifically included in the list of choices. (Setting the hybridization to OTHER where appropriate allows the cleaning function (Refining the conformation) to work optimally.)

Changing the default hybridization type automatically activates the Edit Hybrid tool. If the hybridization type option is already correct, you can activate the Edit Hybrid tool by clicking it.

Changing the hybridization

You can change atoms in the model window to the hybridization type specified in the hybridization type popup in several ways:

• Select the Edit Hybrid tool and then pick the desired atom(s).

• Select the desired atom(s) (Selecting atoms and groups of atoms) and then double-click the Edit Hybrid tool.

You can change the hybridization before adding an atom by using the Add Atom control panel (Precise positioning of atoms during building). You can also edit the hybridization of existing atoms (and other properties simultaneously) with the Edit Selected Atoms control panel (Changing the element type together with other properties).

Editing the structure

Deleting atoms and bonds

Duplicating parts of a model

Examining and changing bond lengths

Examining and changing angles

Examining and changing torsions

Inverting about an atomic center

Translating and rotating atoms

Aligning and positioning atoms

To delete an atom and all bonds leading to it, use the Delete Atom tool in the Sketcher control panel.

You can:

• Select the Delete Atom tool and then pick the atom(s) to delete.

or:

• Select the desired atom(s) and then double-click the Delete Atom tool to delete all selected atoms simultaneously.

• Select atom(s) and then select the Edit/Delete menu item or the Edit/Cut menu item.

• Select atom(s) and then press <Ctrl> <Delete> (simultaneously) while the cursor is in the model window.

To delete a bond between two atoms without deleting any atoms, use the Delete Bond tool.

You can:

• Select the Delete Bond tool and then pick the atoms whose bond you want to delete.

or:

• Select the desired bonded atom pairs(s) and then double-click the Delete Bond tool to delete all bonds between selected atoms simultaneously.

• Delete bonds between all atoms or between selected atoms with the Delete bonds action button in the Edit Connectivity and Bonding control panel. Access this control panel by selecting the Build/Edit Bonds... menu item.

• Delete hydrogen bonds (Hydrogen bonds) between all or selected atoms with the Delete H-bonds button in the Edit Hydrogen Bonding control panel. Access this control panel by selecting the Build/Edit H-Bonds... menu item.

You can also copy or move parts of models, or entire models, from one model space to another (see Moving models between model spaces).

Examining and changing bond lengths

Important

Changing a bond length manually

To change the length of a bond manually, select the Stretch tool in the Sketcher control panel.

Then click two bonded atoms. The length of the bond (in angstroms) is displayed next to it in the model window when you click in empty space. To change the length, click and drag the cursor in empty space in the model window. Dragging up and/or to the right lengthens the bond; dragging down and/or to the left shortens it. You cannot make bonds very unreasonably short or long.

You can also modify bond lengths by moving selected atoms manually (Translating atoms manually). You can also examine bond lengths and other distances with the Measurements control panel (Distances).

Precise change in bond length

To change the length of a bond precisely, select the Move/Bond Geometry... menu item to access the Bond Geometry control panel.

Additional information

Please see the on-screen help for details on using the controls in the Bond Geometry control panel to measure and change bond lengths, valence angles, and torsions and to specify which atoms are moved in the process.

You can also modify bond lengths by translating (Translating atoms precisely) or positioning (Aligning and positioning atoms) atoms to specified locations. You can also examine bond lengths and other distances with the Measurements control panel (Distances).

Default bond lengths

You can change the defaults that Cerius² uses in calculating bonds. To change the default radii of atoms, please see Element properties. For covalent bond calculation preferences, see Bond properties. For setting the hydrogen bond length criterion, see Hydrogen bonds.

Examining and changing angles

Important

Changing an angle manually

To change a valence angle manually, select the Angle tool in the Sketcher control panel.

Then click three contiguous bonded atoms. The angle between them (in degrees) is displayed next to the angle in the model window when you click in empty space. To change the angle, click and drag the cursor in empty space in the model window. Dragging up and/or to the right increases the angle; dragging down and/or to the left decreases it. Angles in rings cannot be changed.

You can also modify angles by moving atoms manually (Translating atoms manually). You can examine angles between any three atoms with the Measurements control panel (Angles).

Precise change in angles

To change an angle precisely, select the Move/Bond Geometry... menu item to access the Bond Geometry control panel.

Additional information

Please see the on-screen help for details on using the controls in the Bond Geometry control panel to measure and change valence angles, bond lengths, and torsions and to specify which atoms are moved in the process.

You can also change angles in the course of translating (Translating atoms precisely), aligning, or positioning (Aligning and positioning atoms) atoms to specified locations. You can also examine angles between any three atoms with the Measurements control panel (Angles).

Default angles

You can implicitly control default valence angles through setting the hybridization state of the atoms involved (Changing the hybridization and adjusting the valence). For setting the hydrogen bond angle criterion, please see Hydrogen bonds.

Examining and changing torsions

Important

Changing a torsion manually

To change a torsion angle manually, select the Twist tool in the Sketcher control panel.

Then click either two or four contiguous bonded atoms. Click two bonded atoms and then click the second atom again to define the bond that you want to twist. Click four atoms to define the specific torsion angle to be changed.

The torsion angle (in degrees) is displayed next to the torsion in the model window when you click in empty space. To change the torsion angle, click and drag the cursor in empty space in the model window. Dragging up and/or to the right increases the angle; dragging down and/or to the left decreases it. Torsions in rings cannot be changed.

You can also modify torsions by rotating parts of models manually (Rotating atoms manually). You can also examine torsions or the angle between any two planes with the Measurements control panel (Torsions).

Precise change in torsions

To change a torsion angle precisely, select the Move/Bond Geometry... menu item to access the Bond Geometry control panel.

Additional information

Please see the on-screen help for details on using the controls in the Bond Geometry control panel to measure and change torsions, bond lengths, and valence angles and to specify which atoms are moved in the process.

You can also change torsions by rotating parts of models to specified orientations (Rotating atoms precisely). You can examine torsions or the angle between any two planes with the Measurements control panel (Torsions). For inverting a chiral center, please see the next section.

Default torsions

You can implicitly control default torsion angles through setting the hybridization state of the atoms involved (Changing the hybridization and adjusting the valence).

Inverting about an atomic center

The most straightforward way of inverting about a chiral center is to use the Invert tool in the Sketcher control panel. (Although inversion can be applied to any atomic center, it should be most useful when the center is chiral.)

You can:

• Select the Invert tool and then pick the atomic center whose chirality you want to invert. Two fragments attached to that atom are rotated 180° about the axis that bisects the bond angle between the fragments. The fragments that are rotated are those that result in the fewest atoms being moved.

or:

• Select the desired atomic centers) and then double-click the Invert tool to invert the chirality at all selected centers simultaneously.

Note

You can examine inversions with the Measurements control panel (Inversions).

Translating and rotating atoms

You can translate selected atoms in all three dimensions by using the mouse to control the cursor in the model window. To translate selected atoms:

• In the x, y plane--Drag the cursor while holding down <Ctrl> and the middle mouse button.

• Along the z axis--Drag the cursor while holding down <Ctrl>, <Alt>, and the middle mouse button.

Tables of mouse button and keyboard combinations are included in Mouse and Keyboard Actions.

Translating atoms precisely

To translate selected atoms a precise distance in a specified direction, select the Move/Atoms Translate... menu item to access the Translate Atoms control panel.

You can specify the direction in Cartesian (XYZ), crystal (ABC), or surface (UVW) coordinates or specify that the direction be calculated as the best-fit vector through the currently selected atoms (not necessarily the same atoms that you select to move).

If symmetry constraints do not allow the requested translation, the closest permitted translation is made instead.

Additional information

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

Rotating atoms manually

You can rotate selected atoms around all three axes by using the mouse to control the cursor in the model window. To rotate selected atoms:

• Around the x axis--Drag the cursor vertically while holding down <Ctrl> and the right mouse button.

• Around the y axis--Drag the cursor horizontally while holding down <Ctrl> and the right mouse button.

• Around the z axis--Place the cursor close to an edge of the model window and drag it parallel to that window edge while holding down <Ctrl> and the right mouse button.

Tables of mouse button and keyboard combinations are included in Mouse and Keyboard Actions.

Rotating atoms precisely

To rotate selected atoms by a precise angle around a specified rotation axis and center, select the Move/Atoms Rotate... menu item to access the Rotate Atoms control panel.

More than one atom should be selected. You can specify the rotation axis and center in Cartesian (XYZ), crystal (ABC), or surface (UVW) coordinates. Alternatively, you can specify that the axis be calculated as the best-fit line through the currently selected atoms and/or the rotation center as their geometric center. (You can change which atoms are currently selected, for specifying each definition.)

If symmetry constraints do not allow the requested rotation, the closest permitted rotation is made instead.

Additional information

Please see the on-screen help for details on the functioning of each control in the Rotate Atoms control panel. You can rotate the selected atom(s) by clicking and dragging a slider or a dial or by entering the angle in the associated entry box.

Aligning and positioning atoms

To accurately align selected atoms with respect to a coordinate system, select the Move/Atoms Align... menu item to access the Align Atoms control panel. You specify one intra-model vector that is to be aligned with one coordinate axis and another intra-model vector to be aligned with a coordinate plane that includes that axis. You also specify the point about which the selected atoms are rotated.

You specify the intra-model vectors to be aligned with the coordinate axis and plane and the rotation center, using Cartesian (XYZ), crystal (ABC), or surface (UVW) coordinates. Alternatively, you can specify that the first intra-model vector (the one to be aligned with a coordinate axis) be calculated as the best-fit vector through the currently selected atoms. Similarly, you can specify that the second intra-model vector (the one to be aligned with a coordinate plane) be calculated as the best-fit vector through the currently selected atoms. You can also specify that the rotation center be calculated as the geometric center of the currently selected atoms. (You can change which atoms are currently selected, for specifying each definition.)

If symmetry constraints do not allow the requested alignment, it is not performed.

Additional information

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

Positioning atoms

To accurately position selected atoms in space, select the Move/Atoms Position... menu item to access the Position Atoms control panel. You specify both a reference point and a destination point, then the selected atoms are moved in a way that maintains their spatial relationship with the reference point (i.e., the reference point is moved together with the atoms).

You can specify the reference and destination points in Cartesian (XYZ), crystal (ABC), or surface (UVW) coordinates and/or specify that these points be calculated as the geometric center of the currently selected atoms. (You can change which atoms are currently selected, for specifying each definition.)

If symmetry constraints do not allow the requested translation, it is not performed.

Additional information

Please see the on-screen help for details on the functioning of each control in the Position Atoms control panel. (You can position atoms while adding them to a model, with the Add Atom control panel, see Precise positioning of atoms during building.)

Refining the conformation

The model structure as initially drawn is usually not chemically reasonable. Thus, it needs to be "cleaned" (i.e., its structure needs to be optimized). Initial optimization is often done with the CLEAN button in the Sketcher control panel. Simply click the CLEAN button and keep the left mouse button depressed until the structure in the model window stops changing. (You can adjust how the clean function works--please see Control of the model-cleaning function.)

You may adjust the structure as desired after you clean it (e.g., Examining and changing bond lengths). However, a better approach may be to apply constraints before additional optimization or to apply symmetry (next paragraph).

Additional optimization

If you want an even more chemically correct structure than the clean function is capable of, you may want to use a forcefield-based minimizer such as the OFF Minimizer or optimize the structure to an energy minimum or a transition state with one of the quantum applications. You can also use the quantum applications to enforce space-group symmetry. Documentation for these modules is supplied separately.

Advanced building and editing

This section tells you where to access some building and editing controls, such as editing atom attributes and changing defaults and preferences, that are not as commonly used as those discussed earlier in this section. It contains information on:

Editing element and bond attributes

Introducing substitutional disorder

Introducing positional disorder

Temperature factors

Control of the model-cleaning function

Related information

Basic building tasks are presented under Basic building and basic editing tasks under Basic editing.

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.

You should already know...

You need to know how to select atoms in your model (Selecting atoms and groups of atoms), so you can edit them. You also of course need to know how to build (Basic building) and edit (Basic editing) a model and/or load a model from a file (Loading model structure files).

You may want to review the basics of how the controls in the Sketcher control panel work (see How it works) or how controls work in general (The Cerius2 Interface).

Editing element and bond attributes

Related information

Changing the properties of individual selected atoms (i.e., not necessarily of all atoms of a given element type) is covered under Changing atoms and their bonding types. Setting temperature factors is discussed under Temperature factors.

You should already know...

You should have already worked with the types of models and the various application modules that you typically use, before deciding whether and how much you should change the default behavior of Cerius². And of course there is no substitute for chemical knowledge and intuition. This section is for experienced Cerius² users.

Element properties

Element properties are stored within Cerius² and used for calculations and display attributes. These properties include mass, van der Waals radius, atomic radius, covalent radius, metallic radius, ionicity, hydrogen bonding nature, and display color. Cerius² "elements" include chemically real elements, "mixture" elements, and "dummy" elements.

Editing element properties

Select the Build/Element Defaults... menu item to access the Edit Elements control panel. Changing element defaults changes the properties for atoms of that element type that already exist in the model, as well as for all atoms added to models later in the current Cerius² session.

Among other properties, you can, for example, change:

• The van der Waals radius that is used in producing BALL displays (Atom and bond display styles) of atoms.

• The atomic radius, which is used by the clean function (Refining the conformation).

• The color used to display an element.

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

"Mixture" elements

Mixture elements are special Cerius² elements (with atomic symbols T, TT, M, and MM) whose properties you can specify as proportions of those of up to eight real elements. Such a mixture can be useful, for example, in studying disordered structures (Introducing substitutional disorder).

Mixture elements are defined using the Element Mixtures control panel, which you access by clicking the Mixtures... pushbutton on the Edit Elements control panel. You can also examine the compositions of predefined mixture elements with this control panel.

Dummy atoms

Cerius² also allows you to use predefined dummy atoms. These nonstandard "elements" (as well as the mixture elements, deuterium and other nonstandard "elements") are listed at the bottom of the Periodic Table window. (You can access the periodic table by clicking the periodic table icon in several control panels, including the Edit Elements control panel.)

Tip

Atom properties

You can also edit properties of individual selected atoms (rather than of all existing and future atoms of a given element type): the element type, hybridization state (Changing the hybridization and adjusting the valence), charge, formal charge, mass, occupancy, the atom name, and temperature factors (Specifying temperature factors). To do so, select the Build/Edit Atoms... menu item to access to the Edit Selected Atoms control panel.

Additional information

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

Most of these atom properties can alternatively be specified before placing an atom in the model window with the Add Atom control panel (Precise positioning of atoms during building).

Bond properties

Editing bonds

Elementary bond editing with the Sketcher and the Edit Connectivity and Bonding control panels is presented under Changing atoms and their bonding types and Editing the structure. These tasks include deleting bonds, changing the bond type and order, and making bonds between selected atoms.

Accessing the tools

For more advanced bond editing tasks or for performing several elementary tasks simultaneously, select the Build/Edit Bonds... menu item to access the Edit Connectivity and Bonding control panel.

You can bond selected atoms or delete bonds, calculate bonding from a connectivity map, change the bond order, and change how resonant bonds are displayed.

Additional information

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

Specifying how bonds are calculated

To define the criteria by which bonds are calculated, click the Preferences... pushbutton to the right of the Calculate connectivity check box in the Edit Connectivity and Bonding control panel to access the Bond Calculation Preferences control panel.

Covalent, general (Slater, i.e., atomic), and (where appropriate) metallic radii are stored for each atom. Depending on the selected Bonding Method, the appropriate radius is used in bond calculations. The stored radii can be edited by specifying an element and method and then entering the radius in the corresponding radius entry box. These radii can also be changed with the Edit Elements control panel (Element properties).

You can also define a Bonding Tolerance (effectively the proportion of the relevant atomic radius to be used in looking for contacts). For example, if the tolerance factor is 1.5 and the ideal bond length is 1.4 Å, a bond is created if the two atoms are within 2.1 Å (1.4 x 1.5) of one another.

You can inhibit the creation of bonds to certain categories of elements (that is, alkali metals, transition metals, and lanthanides/actinides) during bonding calculations using the appropriate check boxes. This inhibition works by effectively zeroing the bonding radius for a given atom. Inhibition of bonding to a specific element can be achieved by actually zeroing the bonding radius for that element.

Additional information

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

Specifying automatic determination of bond types

To specify whether Cerius² should determine the bond types automatically by valence satisfaction, check the Calculate bond types check box. To specify how this algorithm works, click the Preferences... pushbutton next to the Calculate bond types check box in the Edit Connectivity and Bonding control panel to access the Bond Type Calculation Prefs control panel.

Additional information

Please see the on-screen help for details on the functioning of each control in the Bond Type Calculation Prefs control panel.

Calculating bonds

To request bond calculation between all atom pairs that meet the criteria, click the CALCULATE pushbutton in the Edit Connectivity and Bonding control panel. Bonds are added or deleted so that they meet the criteria. Subsequent use of the cleaning function (Refining the conformation) also uses the radii set with the Bond Calculation Preferences or Edit Elements control panel.

Hydrogen bonds

Hydrogen bond criteria

When Cerius² decides which atom pairs to join by hydrogen bonds, it uses these criteria (Figure 1):

• The distance between a potential acceptor atom and a hydrogen atom is less than the distance criterion.

• The angle between a potential donor, a hydrogen, and a potential acceptor is greater than the angle criterion.

Editing hydrogen bonds

Select the Build/Edit H-Bonds... menu item to access the Edit Hydrogen Bonding control panel.

With this control panel, you can calculate, delete, or make hydrogen bonds between all or selected atom pairs, as well as set the color in which hydrogen bonds are displayed in the model window. You can also enable automated recalculation of hydrogen bonds whenever, for example, the model's conformation changes.

Additional information

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

Specifying how hydrogen bonds are calculated

To define the criteria by which hydrogen bonds are calculated, click the Preferences... pushbutton in the Edit Hydrogen Bonding control panel, to access the H-Bond Preferences control panel.

With this control panel, you can set the distance and angle criteria. You can also specify the hydrogen bonding nature of an element, i.e., whether it is a donor, an acceptor, either a donor or an acceptor, or neither a donor nor an acceptor. (The hydrogen-bonding nature of elements can also be changed with the Edit Elements control panel, see Element properties.)

When these criteria are altered, any existing hydrogen bonds that no longer meet the criteria are deleted when you click the CALCULATE pushbutton in the Edit Hydrogen Bonding control panel. Hydrogen bond recalculation occurs automatically if the Enable automatic recalculation check box in the Edit Hydrogen Bonding control panel is checked.

Additional information

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

Calculating hydrogen bonds

To request hydrogen bond calculation between all or selected atom pairs that meet the criteria, click the CALCULATE pushbutton in the Edit Hydrogen Bonding control panel.

Introducing substitutional disorder

Substitutional disorder can be used whenever two elements need to be randomly replaced in a structure. For example, substitutional disorder is particularly useful in dealing with zeolites where you may want to randomly replace silicon atoms with aluminum.

How it works

Substitutional disorder randomly replaces a fraction of the atoms of one element type with atoms of another element type. Substitutional disorder can be applied to the whole model or to only a selected portion of the model. A target ratio is used to set the fraction of the atoms to be replaced.

Löwenstein's rule applies only to the substitution of aluminum. Generally, this rule is used in the random replacing of silicon by aluminum in zeolite structures. Application of Löwenstein's rule ensures that no two aluminum atoms share a common oxygen. This may mean that the target replacement ratio is not met. A message in the text window reports the actual ratio that is achieved.

Nonperiodic and periodic models

Substitutional disorder can be applied to nonperiodic models and to periodic models without symmetry.

Tip

Performing substitutional disorder

To introduce substitutional disorder into a model, select the Build/Disorder... menu item to access the Disorder control panel. You can use this control panel to:

• Apply the substitution to the whole model or to selected atoms.

• Specify what element is to be replaced by what element and the target ratio to be achieved.

For example, you can replace all silicon atoms in a model with aluminum by setting the target ratio to 0 or replace one-fourth of the silicons with aluminums by setting the ratio to 3.0.

• Apply Löwenstein's rule (if you are replacing silicon with aluminum).

Please see the on-screen help for details on the functioning of each control in the Disorder control panel. After the substitution is performed, information on the number of atoms replaced, etc., is shown in the text window.

Introducing positional disorder

Positional disorder is a convenient way to move a model away from a local energy minimum. For example, you can apply positional disorder before cleaning a model (see Refining the conformation) or before performing an energy minimization (see the documentation for the Minimizer module in Cerius² Simulation Tools).

How it works

Positional disorder randomizes atomic positions--atoms are moved by the specified displacement in a random direction. Positional disorder can be applied to any model type. However, if an atom in a periodic structure is in a special symmetry position, it is not moved from that position, although it can be displaced in allowed directions. For example, if an atom lies on a symmetry axis or plane, it (and all its symmetry copies) is moved only along that axis or within the plane, respectively. The distance the atom is moved is the component of the random displacement vector that lies on the symmetry axis or in the symmetry plane.

Performing positional disorder

To introduce positional disorder into a model, select the Build/Disorder... menu item to access the Disorder control panel. You can use this control panel to:

• Apply the disordering to the whole model or to selected atoms.

• Specify the displacement distance (in angstroms) for each atom that is to be moved (in a random direction).

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

Temperature factors

If you need to know only how to work with temperature factors within the Cerius² interface, you may skip this theory section and go directly to:

Specifying temperature factors

Editing temperature factors

Loading and saving temperature factors

Related information

Representing the thermal motions of atoms graphically is discussed under Thermal ellipsoids.

Temperature factors and atomic vibrations

Atomic vibrations are described in the lowest order by their temperature factors. If the deviation of an atom from its equilibrium position is r = (x,y,z), the vibration is characterized by the matrix:

Eq. 1            

Where xy represents the average over many vibrations.

Anisotropic and isotropic temperature factors

H is symmetric and contains six independent quantities, the anisotropic temperature factors U_ij. If the atomic vibration is isotropic, then H reduces to the form x² I and requires just one number (the isotropic temperature factor U_iso) to describe it:

Eq. 2            

Temperature factors are commonly used to describe the effect of vibration on X-ray, electron, and neutron scattering. For the first-order amplitude of scattering from an atom at q = ha* + kb* + lc* in reciprocal space, the scattering amplitude is multiplied by:

Eq. 3            

Several different though equivalent ways of describing the temperature factors exist. (Cerius² can read temperature factors in several formats, see Loading and saving temperature factors.) Sometimes the vibration is described in terms of a crystal lattice coordinate system (a,b,c) rather than a Cartesian one.

Cartesian and crystal coordinate systems

If an atom has coordinates (x,y,z) with respect to the Cartesian axial system and (u,v,w) with respect to the lattice system so that:

Eq. 4            

Table 3 shows the relationship between the different temperature factor forms and the way in which they modify the scattered amplitude.

Table 3. Forms of temperature factor terms

Form	Relationship to H or x2	Scattering amplitude multiplied by
Uiso
Biso
Uij 1
Bij 2
ij 2

1 a* = (b ^ c)/(a· b ^ c), etc. 2 For , the factor of two on the cross terms is included in the term for some structure file formats (please see File Formats for more details).

Temperature factors in Cerius²

Internally, Cerius² stores the atomic vibration matrix H. Cerius² stores isotropic and anisotropic temperature factors for every atom. You decide which of the two types to use for calculation or display.

For isotropic factors, the default format is Uiso. For anisotropic, the default format is U_ij.

Typical applications affected by temperature factors are X-ray, eletron, and neutron diffraction calculations (see separate documentation) and the display of thermal ellipsoids (Thermal ellipsoids).

Specifying temperature factors

With this control panel you can:

• Select ISOTROPIC or ANISOTROPIC to specify whether isotropic or anisotropic temperature factors will be used in any relevant calculation involving the atom to be added.

• Select the format to be used (i.e., B_iso or U_iso for isotropic temperature factors and U_ij, B_ij, or _ij for anisotropic temperature factors; see Table 3).

• Enter the value of the isotropic temperature factor or the values for the anisotropic temperature factors.

The six anisotropic temperature factors are entered as a matrix:

U11     U12    U13
        U22    U23
               U33

Command line

If you specify the anisotropic temperature factors from the command line, you should enter them in the order (1,1) (2,2) (3,3) (1,2) (2,3) (1,3).

Additional information

Please see the on-screen help for details on the functioning of each control in the Added Atom Temperature Factors control panel.

Editing temperature factors

• Select the format to be used (i.e., B_iso or U_iso for isotropic temperature factors and U_ij, B_ij, or _ij for anisotropic temperature factors; see Table 3).

• Enter the value of the isotropic temperature factor or the values for the anisotropic temperature factors.

The six anisotropic temperature factors are entered as a matrix:

U11     U12    U13
        U22    U23
               U33

• Click the Use Isotropic or Use Anisotropic action button to change the temperature factors of the atom to isotropic or anisotropic (using the format and value(s) specified).

If you specify the anisotropic temperature factors from the command line, you should enter them in the order (1,1) (2,2) (3,3) (1,2) (2,3) (1,3).

Additional information

Please see the on-screen help for details on the functioning of each control in the Added Atom Temperature Factors control panel.

Loading and saving temperature factors

The MSI, SHELX, CIF, ICSD, DBWS, and MolEN structure file formats can all be used to store isotropic and anisotropic temperature factors (please see File Formats for more details).

Isotropic temperature factors (but not anisotropic factors) are stored in both .xtl and .car/.mdf files.

Control of the model-cleaning function

You can specify the mode of operation of the cleaning function, the number of cycles performed (for one-shot cleaning), which atoms are to be cleaned, and which atoms are to be taken into account during the clean.

Specifying default behavior of the clean function

Click the Preferences... pushbutton near the bottom of the Sketcher control panel to access the Cleaner Controls control panel.

With this control panel you set preferences to:

• Optimize the positions of all atoms in a model during cleaning or only those of selected atoms.

• Take into account the interactions of all or selected atoms.

• Optimize for a specified number of cycles ("one-shot") each time the CLEAN pushbutton in the Sketcher control panel is clicked or continue optimizing for as long as the mouse button is kept depressed after clicking the CLEAN pushbutton.

• Watch the progress during one-shot cleaning or update the view of the model only after cleaning is finished.

• Clean continuously (i.e., after every sketch operation) without needing to click the CLEAN pushbutton.

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

Other builders

With these builders you can readily build series of analogous structures, crystals and other periodic structures, surfaces, interfaces, polymers, and amorphous structures.

Not all the Sketcher control panel functionality works with periodic systems. Those functions that do work include sketching bonds; changing the element, hybridization, or bond type; editing bond lengths, angles, and torsions; and deleting atoms or bonds.