Cerius2 Modeling Environment

6       Managing Models and Sessions

Among the many functions that you use the Visualizer to perform are management of the Cerius² session and of the models with which you work.

This section explains

This section tells you how to load and save structure files and how to manage Cerius² models and sessions:

Loading model structure files

Handling multiple models

Saving model structure files

Working with Cerius2 sessions

Loading model structure files

This section tells you how to bring one or more models that are stored on disk into your current Cerius² session. These can be models supplied with Cerius² by MSI (see Models supplied by MSI) or models that you or someone else built and saved earlier (Saving individual models).

Related information

Building models is explained in Building Models and demonstrated in Introducing Cerius2. Saving models is discussed under Saving model structure files. File formats are presented in File Formats.

You should already know...

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

Loading models

Select the File/Load Model... menu item (from the main control panel's menu bar) to access the Load Model control panel:

Finding model file(s)

Navigate the directory structure and find the desired file(s):

• To go to a higher-level directory, use the directory selector popup.

The current directory is printed on the popup when it is in its inactive state.

• To return to the directory from which you started Cerius², click the small pushbutton next to the directory selector popup.

• To open a directory that's shown in the file selector list box (including the parent directory, indicated by ../), double-click the directory name.

• To display the names of files having the desired format, set the File Format popup if necessary.

For example, when the File Format popup is set to MSI, *.msi is listed in the filename text entry box (as a filename filter) and only filenames that end with .msi are shown in the file selector list box.

You can also use the filename text entry box to specify a file, directory, or pathname or to set up your own filename filter. Valid UNIX wildcards and operators are allowed.

• If the list of file and subdirectory names is longer than the file selector list box, use the scroll bar on its right to move up and down the list.

To choose the target model space, set Model Space to CURRENT or NEW (see Handling multiple models for information on model spaces).

Note

Loading the model file(s)

There are several ways of selecting and loading the desired file(s):

• To load a single model file, double-click its name in the file selector list box.

or:

Select its name file selector list box (the name becomes highlighted) and then click the LOAD button.

or:

Enter its name in the filename text entry box. (Enter means to type in the name and then press <Enter> or click the LOAD button.)

• To load several model files simultaneously, select their names in the file selector list box and then click the LOAD button.

To select several model files, click the first filename and then drag to select several contiguous filenames, and/or <Shift> click to select a range of contiguous filenames, and/or <Ctrl> click to add a noncontiguous filename. Selected filenames are highlighted.

To deselect filenames, <Ctrl> click to deselect individual filenames or simply click to start again with a single filename.

The mouse/keyboard combinations for selecting and deselecting filenames (which are the same in any control panel that contains a file selector list box) are all described under Mouse actions.

A tutorial example of loading models can be found in Reading in additional models.

Additional controls

You can change how files of a particular format are interpreted as they are read in. For example, whether to use any periodic information contained in the file, whether the number of hydrogen atoms is to be checked and corrected, whether and how to fill in possible missing bonds, etc.

To access these additional controls, click the Preferences... button in the Load Model control panel, which gives access to the Load Preferences control panel. The controls displayed in this panel depend on what the File Format popup in the Load Model control panel is set to.

Additional information

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

Models supplied by MSI

Cerius² supplies databases for a wide range of types of molecules and materials. These databases are contained in subdirectories of the Cerius2-Models directory (accessible from your run directory during Cerius² sessions). These subdirectories include models of catalysts, ceramics, metals, minerals, molecular crystals, monomers, organics, polymers, sorbates, and others.

File formats

Many file formats besides the MSI format (see File Formats) can be imported if you need to use model files obtained from other programs or databases. However, transfer of all model data cannot be guaranteed when reading files that are not in MSI format.

Handling multiple models

Cerius² can hold many models at one time, each in its own model space. This section tells you how to work with several models that are present simultaneously in the same Cerius² session. The number of models allowed depends only on your computer's memory limitations.

Finding information

This section includes information on:

Basic model management tasks

Moving models between model spaces

Related information

Building models is explained in Building Models and demonstrated in Introducing Cerius2. Loading models is discussed under Loading model structure files.

You should already know...

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

Basic model management tasks

When you have several models present simultaneously in the same Cerius² session, you need to know how to make a model be "current" so you can work with it. You may also want to know how to display one or more models, name models, open a new model space in order to load or build another model, etc.

Finding information

This section includes information on:

Creating, clearing, and deleting model spaces

Specifying the current model

Selecting model spaces

Controlling model visibility and the display mode

Renaming models

Sorting model table entries

The model manager

The model manager is part of the main control panel. When a Cerius² session is started with an empty model space (the usual default startup), the model manager looks like:

Additional information

Please see the on-screen help for details on the functioning of each control in the model manager.

Creating, clearing, and deleting model spaces

When do you need to add model spaces?

However, for example, builders have no way of knowing when you may want to start a new model. They therefore assume that you want to continue modifying an existing model until you inform them otherwise.

Creating an empty model space

To add an empty model space, click the add model space tool in the model manager. The new model space's name is added at the bottom of the model table.

Clearing a model space

You may want to replace an existing model with a new one or perhaps realize you've built or loaded an incorrect model. Clearing a model space removes the model but allows its now-empty space to remain in the model manager.

To clear a model space, click the clear model space tool in the model manager. If no model space(s) are selected (Selecting model spaces), the current (Specifying the current model) model space is cleared.

For many models, you can also select (Selecting atoms and groups of atoms) all the atoms of the current model and delete them (Deleting atoms and bonds) to clear the current model space. (Nonatomic information, if any, is not removed by this method.)

Deleting a model space

If you want to delete both the model and the space that contains it, click the delete model space tool in the model manager. If no model space(s) are selected (Selecting model spaces), the current (Specifying the current model) model space is deleted. The last remaining model space cannot be deleted.

Example

A tutorial example of adding and deleting model spaces is found under Managing multiple models.

Specifying the current model

Setting the current model

To specify that a certain model be current, click the current model indicator (diamond-shaped button) to the left of its name in the model table. The current model is identified by a red diamond; all other diamonds are greyed out.

Alternatively, you can press <Ctrl> on the keyboard and click any atom in the desired model with the left mouse button.

The current model is always visible in the model window, as the only model in the model window, in the lower left corner of a multi-paned model window displaying many models in grid or border mode (Controlling model visibility and the display mode), or as one of the models displayed in overlay mode (Controlling model visibility and the display mode).

Example

A tutorial example of handling multiple models is found under Managing multiple models.

Selecting model spaces

• On which to perform model management operations.

• To be used by various application modules.

To select model spaces, click the model ID number(s) in the model table, using the left mouse button. A single click selects only one model. You can select more than one model or change what is selected:

• To select several models, click the first model ID number and then drag to select several contiguous models, and/or <Shift> click to select a range of contiguous models, and/or <Ctrl> click to add a noncontiguous model name. Selected model rows are highlighted.

• To deselect models, <Ctrl> click to deselect individual models or simply click to start again with a single model.

Controlling model visibility and the display mode

Which models are visible

Use the visibility indicators (square buttons) to the right of the model names to control which models are visible.

• Click one or more of the visibility indicators to toggle the models between being visible (cyan, pyramidal visibility indicators) and hidden (empty visibility indicators).

• Show all models, or all selected models, by clicking the set to visible button on the top row of the model manager.

and/or:

• Hide all models (except the current model), or any selected models (except the current model), by clicking the set to invisible button.

How they are displayed

The overlay mode, grid mode, and border mode display tools control how the model spaces are displayed in the model window:

• Border mode--To divide the model window into one large pane (located in the lower left corner, and which displays the current model) surrounded by a border of 5 smaller panes, select the border mode tool. If only the current model is visible, it fills the entire model window.

• Grid mode--To divide the model window into 4, 9, 16, ... or 81 equal-sized panes (with the current model in the lower-left pane), select the grid mode tool. As many panes appear as are required to contain the visible models. If only the current model is visible, it fills the entire model window.

• Overlay mode--To display all visible models together in the same (large) model window, select the overlay mode tool. Although they are displayed together on the computer screen, the models still occupy separate model spaces.

A tutorial example of handling multiple models is found under Managing multiple models.

The following picture shows a model table with one current model that is implicitly visible (ID = 8), several visible models (IDs 4, 5, 7, 8), several invisible models (IDs 6, 9, 10), several selected model spaces (IDs 5, 6, 9), and one model that is being renamed (ID = 10), with scrolling needed to see the whole list):

Renaming models

You can rename models by clicking the existing name, then typing a new one and pressing <Enter> (or clicking somewhere else on a control panel).

Example

An example of renaming a model is given under Reading in more models.

Sorting model table entries

Sorting criteria

To select the criteria by which models in the model table are sorted, select the appropriate control:

• The ID tool--Sort model table entries in ascending order according to the model ID number. These numbers are assigned serially as new model spaces are created. They cannot be reassigned during the current session and are not reused if a model space is deleted.

• The current (diamond) tool--Place the current model at the top of the model table and sort all other models in ascending order by model ID number.

• The name tool--Sort model table entries alphabetically by name.

• The visibility tool--Place all explicitly visible models at the top of the model table (sorted in ascending order by model ID number), followed by the current model (if it is not explicitly visible), followed by all invisible models (sorted in ascending order by model ID number).

This section includes information on:

Copying whole models from one model space to another

Moving parts of models from one model space to another

Copying models to and from other applications

• You can copy a model into an empty current model space, for example, to use it as a base for additional building operations.

• You can also copy a model into a current space that already contains a model so as to build up a composite model. (The formerly separate models are now considered one model.)

The simplest way to copy a whole model to a new model space is to make sure the desired model is current, then select (in order) the Edit/Copy and Edit/Paste menu items. A new model space is created automatically.

If you have the display in border mode (How they are displayed) anyway, make sure the correct model is current (Specifying the current model). Then simply click in empty space within a border pane whose contents you want to copy and drag the cursor into the current model space's display pane (lower left of the model manager). (Clicking an atom in a border pane selects that atom, Selecting atoms in several models.)

You can also select all atoms in a model and use cut (or copy) and paste (Moving parts of models from one model space to another) to move entire sets of atoms from one space to another. (Nonatomic information, if any, is not copied by this method.)

Example

A tutorial example of copying model-space contents from one space to another can be found under Copying models from one model space to another.

Moving parts of models from one model space to another

• To remove selected atoms from the current model, select the Edit/Cut menu item or press <Alt> x on the keyboard. These atoms can then be pasted into the same or another model space.

• To make a copy of selected atoms from the current model, select the Edit/Copy menu item or press <Alt> c on the keyboard. These atoms can then be pasted into the same or another model space.

• To paste atoms (that were previously cut or copied from the same or a different model space) into the current model space, select the Edit/Paste menu item or press <Alt> v on the keyboard. If all the atoms to be pasted correspond to atoms in the current model, they are pasted to an offset position.

Important

Copying models to and from other applications

Timeout period

Transferring large models between Cerius² and other applications can take up to a minute or more. Cerius² is configured to wait up to 3 min for information pasted from other applications to complete transfer. However, transferring large models or structural elements from Cerius² to other applications may fail if the other application's timeout value is not increased. The default timeout period for most applications' paste operations is 5-30 s, depending on the operating system. If you have problems pasting large models from Cerius² to other compatible programs, you can usually increase the other application's timeout value by adding an entry to the .Xdefaults file in your home directory. For example, to increase the timeout value for SGI's InPerson application add the following entry:

InPerson*selectionTimeout:       180000

Cerius2*selectionTImeout:       180000

This section tells you how to save one or more models that are in your current Cerius² session, to store them on disk. You will probably want to save models that you have built or modified and may want to use again. You should save your model before running any calculation or performing other activities that might change its conformation, if the original conformation of your model is important.

Finding information

This section includes information on:

Saving individual models

Saving all models

Building models is explained in Building Models and demonstrated in Introducing Cerius2. Loading models is discussed under Loading model structure files. File formats are presented in File Formats.

You should already know...

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

Use of the file selection list box and other file selector controls to navigate the directory structure is presented in detail under Finding model file(s).

How to make a model be the current one is described under Basic model management tasks.

Saving individual models

You may want to create your own directories or subdirectories in which to save models. For example, you may want to save models relating to a specific project together or save related models as a database.

To do so, go to a UNIX shell window (not the one from which you are currently running Cerius²), cd to the desired parent directory, and create your subdirectory with the UNIX mkdir command. (This can be done at any time.) For example:

>	cd ~/CeriusRuns

>	mkdir myModels

Saving the current model

Select the File/Save Model... menu item (from the main control panel's menu bar) to access the Save Model control panel. This control panel is used to save the current (Basic model management tasks) model.

Use the file selector controls in the Save Model control panel to move through the file system to the directory in which you want to save the current model. (Newly created directories appear in the file selector list box when the appropriate parent directory is opened or reopened with the file selector controls or when the control panel is opened.)

After selecting the appropriate directory, specify a name for the structure file by typing that name in the file name entry box, then press <Enter> or click the SAVE button.

A warning helps prevent you from accidentally overwriting existing structure files. (You may choose and enter an existing filename if you want to overwrite an existing structure file.)

Example

A tutorial example of saving one model is given on Saving a model.

Additional controls

You can save files in a non-Cerius² format. Some formats allow a choice of formatting options. To set them, click the Preferences... pushbutton to accesses the Save Preferences control panel. The controls displayed in this panel depend on what the Save format popup in the Save Model control panel is set to.

Saving part of a model

If you want to save only part of a model, select the desired part (Selecting atoms and groups of atoms), cut or copy it and paste it into a new model space (Moving parts of models from one model space to another), and save the new model.

Additional information

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

What is saved as a model

Model data that can be saved to file include atom coordinates (Cartesian, fractional, or internal), element type, charge, bonding connectivity, crystal unit cell, crystal symmetry, occupancy, and temperature factors. The exact combinations depend on the format you select from the Save Format popup in the Save Model control panel. The default MSI file format holds all model data.

File formats

Cerius² has its own model-file format (.msi format) capable of storing every detail of any model in the Cerius² modeling environment. You should always store your model files using the .msi format unless you want to exchange them with databases, other molecular modeling applications, or your own programs.

Many file formats besides the .msi format (see File Formats) can be written if you need to transfer model files to other programs or databases. However, transfer of all model data cannot be guaranteed when writing files that are not in .msi format.

Saving all models

Working with Cerius2 sessions

This section tells you what Cerius² sessions are and how to start, resume, and save them. It is useful if you, for example, want to:

• Resume a session that you had to interrupt earlier.

• Save all your models at once.

• Return Cerius² to its start-up state.

• Always start your sessions with Cerius² in a certain state.

Finding information

This section includes information on:

Starting a new session

Saving the current session

Loading a previously saved session

Using saved sessions as preferences settings

You should already know...

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

Use of the file selection list box and other file selector controls to navigate the directory structure is presented in detail under Finding model file(s).

What is a session?

A Cerius² session consists of all the models and data with which you are currently working, as well as application preferences that you have specified.

Starting a new session

To start a new session, select the File/New Session menu item. Clicking Confirm in the message window that appears reinitializes Cerius², which is equivalent to quitting and restarting Cerius².

Important

Saving the current session

Making custom directories

You may want to create your own directory or subdirectory in which to save your session.

To do so, go to a UNIX shell window (not the one from which you are currently running Cerius²), cd to the desired parent directory, and create your subdirectory with the UNIX mkdir command. (This can be done at any time.) For example:

>	cd ~/CeriusRuns

>	mkdir tutorialSession

Select the File/Save Session... menu item (from the main control panel's menu bar) to access the Save Session control panel. This control panel is used to save the current session.

Use the file selector controls in the Save Session control panel to move through the file system to the directory in which you want to save the current model. (Newly created directories appear in the file selector list box when the appropriate parent directory is opened or reopened with the file selector controls or when the control panel is opened.)

After selecting the appropriate directory, specify a name for the session file by typing that name in the file name text entry box, then press <Enter> or click the SAVE button.

A warning helps prevent you from accidentally overwriting existing session and model files. (You may choose and enter an existing filename if you want to overwrite an existing session file.)

What is saved as a session

A saved session consists of a session file (.mss file extension) and a set of standard MSI-format structure (model) files. When you save a session, one model is written in the specified directory for each occupied model space. The session file contains application preferences, customizations, any cross-model linkages, and references to the saved structure files.

Related information

Saving individual models is described in Saving model structure files.

Loading a previously saved session

What resuming a session does

When you load a saved session, the current session is reinitialized (i.e., unsaved models and data are lost and settings return to their defaults), all models referenced by the resumed-session file are loaded into model spaces, and application preferences are set to the values indicated in the resumed-session file.

Resuming a session

Select the File/Load Session... menu item (from the main control panel's menu bar) to access the Load Session control panel. This control panel is used to load the session you want to resume.

Use the file selector controls in the Load Session control panel to move through the directory system to find the session you want to resume.

Either double-click the name of the desired session file or select the desired session file and click the LOAD button. You can also enter its name in the session name text entry box.

Important

What next?

You can now resume work from the point at which you saved the session you just loaded.

Related information

Loading individual models is described in Loading model structure files.

Using saved sessions as preferences settings

Saving preferences in a session file

Nondefault application settings are saved when you save a session (What is saved as a session). (However, not all applications save all nondefault control settings when a session is saved.)

You may want to start up one of your typical sessions by changing all settings as desired, in the absence of any models. Then you can save this "empty" session.

Although you can load only the preferences from any session file, saving an empty session may, depending on how you work, decrease disk space requirements.

Loading only preferences from a saved session

Before loading or building any models, load your preferences by:

• Loading (Loading a previously saved session) an empty session file.

or:

• Checking the Preferences Only check box in the Load Session control panel and then loading any desired session file.

Warning

Related information

Information on controlling Cerius² from prerecorded command scripts is given in Controlling Cerius2 from scripts.

Other customization activities are covered in Customizing the Interface.