Introduction to Catalyst

Contents of this page:

Catalyst workbenches
Catalyst objects
Selecting objects
Moving objects and icons
Performing actions upon objects

Other questions you may have: How do I . . .

The terminology, presentation, and operations within Catalyst are intended to be similar to a laboratory environment. Catalyst includes several work areas that you can configure to your preference and use to create and manipulate molecules, hypotheses, spreadsheets, and chemical information.

At the top of the screen you see the Stockroom, where you keep data such as databases and other objects. In the Stockroom you can create a separate lab for each project, where a lab is a way of associating and organizing spreadsheets, compounds, and hypotheses relating to a given project.

Along the top of the Stockroom, immediately below the menu bar, is the toolbar, which contains five buttons. The name of each button is displayed in the help area at the bottom of the Stockroom when the cursor is placed over the button. See Using the toolbar.

Use the buttons in the toolbar to open the Catalyst Workbenches and their associated toolsets. Use the Exit button to quit from (and optionally save) your current Catalyst session.

Catalyst workbenches

The View Compound workbench allows you to "synthesize" a compound, view it in two and three dimensions, perform minimization to determine an energetically reasonable 3D structure, and generate and inspect a conformational model for the compound. Associated with the View Compound workbench is a dynamic Periodic Table from which you can select elements for use in creating molecules. At the bottom of the Periodic Table is a menu of common chemical groups and substituents for viewing and editing in both 2D and 3D. See Tasks you can do in the View Compound workbench.
You can use the View Database workbench to browse and search databases containing 3D, 2D, and 1D compound data (properties). You can search databases or spreadsheets for compounds matching a specified hypothesis. See View Database Workbench.
With the View Hypothesis workbench you can construct a hypothesis in 3D with features from the Feature Dictionary or add features using a template molecule. You can also bring a hypothesis generated in the Generate Hypothesis workbench into View Hypothesis to edit. You can compare hypotheses structurally and functionally with molecules or with other hypotheses. See View Hypothesis Workbench.
With the Generate Hypothesis workbench you can automatically generate and analyze a hypothesis from a representative set of lead compounds that have biological activity data. The output hypothesis provides estimated activities associated with the common features in the hypothesis. You can use a generated hypothesis to fit to other lead compounds or to search a database for additional compounds with similar structures. See Generate Hypothesis Workbench.

Workbench functional areas

Above is a typical 2D/3D editing workbench with the functional areas identified. Each workbench has five to seven functional areas:

A shelf for storing objects (such as hypotheses, databases, spreadsheets, compounds).
A menu bar with drop-down menus for selecting actions.
A toolbox with drawing and object-manipulation tools.
One or two configurable workspaces for drawing, editing, analyzing, and viewing molecules and hypotheses in 2D and 3D.
A QuickTool area with special functions (such as the View Compound QuickTool).
In the View Database and Generate Hypothesis workbenches, a tabular report area to create and edit spreadsheets and reports.
A status area for displaying current results and other transient information from actions.
A one-line help area for displaying a brief description of the object on which the mouse cursor rests.

See the individual workbench descriptions for more detail about each of the functional areas in that workbench.

Catalyst objects

Catalyst has several types of objects that you can use to perform molecular modeling and analysis tasks. Menu items, control panels, and toolbar buttons operate on objects, which are characterized by their unique sets of associated properties. For example, a compound is a Catalyst object that has unique properties such as topology and molecular weight. The available types of Catalyst objects are compound, database, spreadsheet, hypothesis, workbench, lab, and journal:

Compound A molecule with associated characteristics and descriptive information. Each Catalyst compound has a name, topology (atom connection list), stereochemical properties, and both 3D representations (one or more conformers) and 2D representations (flats).
Each compound must have a unique name. A compound also has associated physical properties, such as molecular weight and biological activity. Each displayed instance can be assigned special display properties, such as color-coding of particular atoms. In Catalyst the terms molecule and compound are used interchangeably.

Database A set of data describing a group of compounds and their properties. Catalyst can provide access to a Catalyst version of your corporate compound database. Catalyst compounds and hypotheses are saved to the StockroomDB that can be browsed and searched.

Spreadsheet A collection of data for a set of related compounds. Spreadsheets are used to store and display the results of database searches and to store input and output data for hypothesis generation. Information can be displayed in one of several report styles. Spreadsheets can be browsed, searched, edited, printed, exported and imported.

Hypothesis A specification of the distinguishing characteristics for a related set of compounds. Hypotheses can include topological and atomspecifications, property specifications, geometrical constraints, derived geometric objects, and high-level chemical functionality definitions.
You can interactively create the significant features of a hypothesis, and then modify and use the hypothesis in other operations, such as database searches.
Also, Catalyst can automatically generate a hypothesis for a set of related compounds by analyzing their structural and chemical properties and relating them to their biological activities. You can fit a hypothesis to the conformers of a sample molecule, evaluate the fit, and estimate the molecule's activity.

Workbench Icon A set of work areas containing Catalyst objects and commands, and workspaces in which to use them. Analogous to the workbench in a chemist's laboratory, each workbench has its shelf for materials (compounds, databases, spreadsheets, hypotheses) and its own set of tools with which to operate on the materials. Active and iconified workbenches have icons in the Stockroom or lab from which they were opened.

Lab An object that you define and fill with compounds, databases, spreadsheets, hypotheses, and other labs related to a specific project or line of investigation. A lab is like a traditional file folder: it is the main context for organizing information.

Journal (no icon) A text record of the operations and Catalyst messages that occur during a session. The journal can be used to recreate a Catalyst session. The last three journals are saved automatically in separate files.

Local objects

Several operations in Catalyst create a local object, a temporary version of a compound, hypothesis, or spreadsheet that can be used only in the workbench in which it was created. It cannot be dragged to any other workbench or lab. It can be dragged to a QuickTool associated with the workbench.

A local object on a workbench shelf looks the same as a saved object, except that its icon ID has an L in the center, and its name is of the form Local-n, where n is a number to distinguish multiple local objects of the same type on the shelf.

To change a local object to a regular Catalyst object, select its icon on the shelf and select the Data/Save To Lab As menu item. After saving the local object, a regular icon replaces the local-object icon on the shelf, with the name you gave it. If a local object is not saved, it is discarded when you close its workbench.

Operations that create local objects in a workbench include:

Creating new molecules or fragments in the View Compound QuickTool and returning to the main workbench places a local molecule on the shelf for each fragment created.
Building new hypotheses in the View Hypothesis QuickTool and returning to the main workbench places a local hypothesis on the shelf for each new hypothesis.
Searching or browsing a database creates a local spreadsheet containing the hits.
Performing a Regress Hypothesis action in the Generate Hypothesis workbench creates a local hypothesis.
Creating a hypothesis in the Exclude/OR editor creates a local hypothesis when you return to the parent View Hypothesis workbench.
Creating or modifying property data in a hypothesis that has only 1D values (no 2D or 3D information) creates a local 1D hypothesis.

Selecting objects

To use a Catalyst tool or function, generally you first select the object or objects on which you want to act, as described below. After you select one or more objects, you use a tool or function to manipulate them. Primary Catalyst objects are compounds (molecules), labs, databases, hypotheses, and spreadsheets (see Catalyst objects for a detailed description). You can select and move the icon representing an object from one work area to another (between the Stockroom, a workbench, and a lab, for example). You also can select and move a molecule or hypothesis within a 2D/3D workspace.

Note: Descriptions of object selection apply to the three-button mouse. If you prefer one-button mode, press the left mouse button and <Shift> on the keyboard instead of the middle mouse button, and press the left mouse button and the <Ctrl> key instead of the right mouse button.

To select an object on the shelf or in the workspace

Move the mouse cursor over the object to be selected.
Press and release the left mouse button (in other words, click the object).

The object is highlighted and selected. No other objects remain selected or highlighted.

To select all components of an object

You can select all atoms and bonds in a molecule for example, in this way:

Move the mouse cursor over one component of the object to be selected -- for example, one atom or one bond of a molecule.
Press and release the left mouse button twice rapidly (in other words, double-click the object).

The entire object is highlighted and selected.

To add objects to those already selected (extend-select)

Move the mouse cursor over the next object to be selected.
Press and release the middle mouse button. (Or, hold down the <Shift> key, left-click the object, then release the <Shift> key.)

The new object is highlighted and selected. Previously selected objects remain highlighted and selected.

To remove objects from those selected (extend-deselect)

Move the mouse cursor over the object to be deselected.
Press and release the middle mouse button.

Catalyst removes the highlight and the object is no longer selected. Previously selected objects remain highlighted and selected.

Selecting groups of objects in a region of a workspace (region-select)

To select a group of adjacent objects in a workspace, use the region-select technique by drawing a rectangle enclosing the objects:

Move the cursor to one corner of a rectangular region containing the objects to be selected (but not on top of an object) in the 2D or 3D workspace.
Press and hold down the left mouse button.
Drag the cursor to the opposite corner of the rectangular area containing the objects you want.
When the rectangle completely encloses all objects to be selected, release the mouse button.

All objects inside the defined rectangle are selected and highlighted. All other objects are deselected.

Region-select toggle

If you use the middle mouse button to draw a selection rectangle, the selection status of all enclosed objects is toggled. That is, objects that were previously selected within the region are deselected, and objects that were previously deselected are selected. All objects outside the rectangle remain either selected or deselected as they were previously.

Deselecting all selected objects

To deselect (remove the highlight from) all selected objects in the workspace, click the Deselect tool in the toolbox.

Another way to remove the highlight from all selected objects is to draw an empty region-selection rectangle:

In an empty area of either workspace, press and hold down the left mouse button.
Drag the cursor to the opposite corner of a small rectangle not containing any objects and release the mouse button.

Catalyst removes all highlights and no objects are selected.

Moving objects and icons

You can move objects between the Stockroom, labs, and workbenches by the drag and drop method:

Place the cursor over the icon of the object to be moved.
Press and hold down the left mouse button. The cursor changes to an image associated with the type of object being moved. (For example, when moving a compound, the cursor becomes a flask.)
Move the cursor to the intended destination and release the mouse button.

The icon for the moved object appears in the new location. If you want the object to be displayed in the new location, drop the icon onto the workspace or the spreadsheet. If you just want the object to be on the shelf, drop the icon onto the shelf.

An object moved from the Stockroom or a lab to a workbench shelf is actually a copy of the object, which remains in its original location. See View Compound Workbench for more details.

Performing actions upon objects

Within Catalyst you perform tasks by specifying an object and an action, usually in that order. First select the object, then select an item from a menu or click a toolbox button to perform the action. For example, to get rid of a compound you have previously saved to the shelf of your workbench, select the icon for the compound you want to remove, then select the Data/Dispose from Workbench menu item.

Some menu items have associated submenus. For example, highlighting the View Compound Tools/Flip 2D menu items opens a submenu containg the items ...about Vertical Axis and ...about Horizontal Axis. Menu items that lead to submenus are indicated by an arrow next to the item name.

Menu items that are followed by ellipses (...) open control panels when you select them, which allow you to make additional choices about how to perform the action.

Note: Commands or buttons that are grayed out are not relevant to the current situation and are therefore not available.

To perform an action accessed from a menu item

Select the object or objects on which you want to act.
Place the cursor over the name of the menu you want.
Click the menu name and hold down the mouse button to display the list of menu items.
Drag the cursor down the menu and release the button to select the item you want. (Note: If the menu item has a submenu, move the cursor to the appropriate submenu item before releasing the button.)
The selected action is performed immediately or a control panel is opened.
If selecting the menu item opens a control panel, select the appropriate controls with the cursor and enter the necessary information in the boxes. Then click the appropriate button at the bottom of the control panel to perform the action.

Another way of selecting menu items

Instead of leaving the mouse button down and dragging to select a menu item, you can click the menu name, release the mouse button, and then click the desired menu item.

To use a toolbox button

Select the object or objects on which you want to act.
Move the mouse cursor over the toolbox button you want and click it.
The action is performed.

For more information, see: View Compound Toolbox or View Hypothesis Toolbox

Token licensing in Catalyst

Licensing for Catalyst employs several different kinds of tokens. The Catalyst functionality that is available to you is determined by the availability of the appropriate types of tokens described in the following sections.

Floating view tokens

Floating view tokens provide interactive access to Catalyst. A floating view license is available to anyone. A view token grants access to all of Catalyst's functionality as enabled by the tokens described below.

Hypothesis tokens

Each hypothesis token allows you to run one background process: hypothesis generation or conformational model generation. Moreover, the presence of one or more hypothesis tokens also enables the following Catalyst functionality:

View Compound workbench
View Hypothesis workbench
Generate Hypothesis workbench

Note that the functionality enabled by a hypothesis token does not tie the token up; that is, the token is also available for background processes (hypothesis or conformational model generation).

Database server tokens

Each database server token allows you to run one process on the local network to service database search requests. The presence of one or more of these tokens also enables the following Catalyst functionality:

View Database workbench
Install Database and Deinstall Database commands in the Stockroom

Database info tokens

Database Info tokens embellish the functionality enabled by a database server token. Each Info token lets you execute a command with the catSearch program to perform background database searches or execute a command with the catDB program to build databases or perform other types of database administration. The presence of one or more of these tokens also enables the following Catalyst functionality:

Create Database... command in the Databases menu of the View Database workbench
Commit 1D Changes to Database command in the View Database and Generate Hypothesis workbenches
Edit Property Dictionary command in the Stockroom

Database access tokens

A database access token comes with each database purchased. If you attempt to open a database when no database access token is available, Catalyst displays an Alert message advising you that no licenses are available for accessing it.

Program and task behavior regarding tokens

Descriptions of program or task requirements for tokens follow. The behavior of each program or task is also documented.

Catalyst

When you initiate Catalyst, the program first tries to obtain a valid view license. Catalyst will not start if no view tokens are available, and it displays a message to that effect. When Catalyst obtains a view token, it retains it until the session ends.

At start-up Catalyst also searches for hypothesis, database server, and database Info tokens although it does not try to obtain them. If the program finds at least one hypothesis token, it enables the functionality described under Hypothesis Tokens above. Similarly, if Catalyst finds at least one database server or database Info token it enables the functionality described under Database Server Tokens and Database Info Tokens above. If none of these tokens are present, Catalyst will not start.

When you attempt to open a licensed database, Catalyst tries to obtain a database access token for that database. Finding a valid token initiates the search or browse. If no valid database access token is found, Catalyst issues an Alert message to that effect.

Hypothesis and conformational model generation in the background

When you set up a background process to generate a hypothesis or a conformational model, one hypothesis token must be available for each process you initiate. The token for each background process is held until the process has terminated.

Database building and maintenance with the catDB program

To activate the catDB program, one database Info token must be free. If no tokens are available, the program issues a message to that effect and will not execute. The catDB program holds the database Info token until catDB finishes processing.

Database searching in the background with the catSearch program

The catSearch program locates and holds a database Info token until searching or browsing is complete. Finding a valid token initiates the search or browse.

catDisk database server program

When the catDisk database server program comes up during Catalyst system startup, the program searches for one database server token. If there are no tokens available, catDisk will not start and issues a message to that effect. If a token is available, catDisk holds it until the program terminates. Once started, the catDisk program runs indefinitely in the background.

What happens if there are not enough tokens?

When you start Catalyst. If there are no floating view tokens available when you attempt to start Catalyst, a dialog box advises you of the situation. It also displays the system user names of persons currently using floating view tokens. You can select the Try Again button to see if a floating view token has become available, or you can select Cancel and try to bring up Catalyst at a later time. A floating view token becomes available when the person using it exits Catalyst.
When you set up a background process. Catalyst warns you if there is no hypothesis token available when you set up a background process (such as generating a conformational model or a hypothesis). Although you cannot run the background task immediately because no token is available, you can still schedule it to start later. There is no way to guarantee that there will be a token available to run a background process at a particular time in the future. However, if you schedule your background process to run at a time when you expect Catalyst usage to be low, it will improve the chances that your process will start successfully at the appropriate time. If a token is not available then, your process will wait until one is.
When a background process starts. A background job tests for token availability when it starts. If a token is not available, the scheduled job is put on a waiting list that remains in effect indefinitely. The job's status is listed as WAIT in the Process Information dialog box, and the number of jobs ahead of it on the waiting list is displayed in parentheses. When tokens become available, the first background job on the waiting list is processed, then the second, and so on. If your background process continues to wait when tokens should be available, you should view the log file (as described in To View the Status of a Background Process) to see if there is some other trouble (such as a problem with the FlexLM licensing server). That is, because the token waiting list stays in effect indefinitely, you need to check the log file to make certain that token unavailability is what is truly preventing your job from running or to diagnose some other problem.
If you persistently receive messages to the effect that tokens are unavailable, see
Your system administrator, who can assist you if something is wrong with your particular system.
MSI Technical Support to help you with problems arising from incorrect configuration.
MSI Sales when the problem is caused by an insufficient number of tokens, and you need to purchase more to support your level of usage.

For detailed technical information about Catalyst licensing, see The License Server Environment in Preparing Your System for Catalyst and Installing and Maintaining Keys in Installing and Maintaining Catalyst.

Displaying Catalyst on a Macintosh X terminal

Introduction

Catalyst can be run on an SGI host machine and displayed on an appropriately equipped Macintosh machine connected to the Ethernet network. With the Mac, the full functionality of Catalyst is available on a lower cost display terminal, using MacX X Window software and an Ethernet card. Catalyst runs on the Macintoshas an X Window application, while the files are saved on the SGI host machine.

See the Notes section in the Tutorials binder for the following information about using a MacintoshX terminal to display Catalyst:

Hardware and software requirements
Installation and configuration procedures
How to run Catalyst with MacX

Function key differences in using a Macintosh

Running Catalyst via MacX is the same as on an SGI workstation except for a few features involving the keyboard function keys and the mouse buttons, as described in this section.

Also, to copy and paste SMILES between X windows, see the section Copy and Paste Functionality on a Macintosh.

Warning: Do not use the standard Macintosh Option key (Alt), or Command key (apple) while in Catalyst.

The middle and right mouse button functions on the SGI machine are mapped to the Macintosharrow keys in the X terminal implementation, as shown in the table below.

Function Macintosh keys SGI keys

Select mouse button left mouse

Extend Select left arrow middle mouse

Rotate right arrow right mouse

Control down arrow Ctrl

Alt up arrow Alt

See the below for a diagram of the important Catalyst functions accessed with the arrow keys.

Function	Macintosh keys	SGI keys
Select	mouse button	left mouse
Extend Select	left arrow	middle mouse
Rotate	right arrow	right mouse
Control	down arrow	Ctrl
Alt	up arrow	Alt

The extend-select and rotate functions for Catalyst are mapped to the Macintosharrow keys as shown below.

Copy and paste functionality on a Macintosh

You can copy and paste molecules in the form of SMILES between MacintoshX terminal windows and Macintoshapplications such as ChemDraw PlusTM on a machine running Catalyst via MacX, as shown in the two tables following. An easy way to get a molecule into Catalyst is to type or select its SMILES string in an X window, copy the string, then paste it into the View Compound workbench.

Note:no types of objects other than SMILES strings can be cut and pasted. However, in the View Compound workbench, the SMILES string for a molecule you want to Copy is derived from its 3D structure selected in the workspace, while a SMILES string you want to Paste is expanded into its 3D structure and displayed in the workspace.

Note: SMILES copied from Catalyst and pasted are stereochemical SMILES (see Writing Catalyst's Stereochemically Extended SMILES), while SMILES copied from other sources and pasted are in standard format.

In addition, you can copy a screen image to the Macintoshclipboard from an X window application (such as Catalyst) using the Macintosh Copy Screen to Clipboard command. Then you can paste the image into a Macintoshapplication such as a word processor or a presentation program.

To copy SMILES strings on a Macintosh X terminal

In this environment	Copy using this function
ChemDraw PlusTM	Copy SMILES command
Macintoshapplication	MacintoshCopy command
X terminal window	X-copy (select SMILES string with left mouse)
View Compound workbench	Copy command (Edit menu)

To paste SMILES strings on a Macintosh X terminal

In this environment	Paste using this function
View Compound workbench	Paste command (Edit menu)
Macintoshapplication	MacintoshPaste command
X terminal window	X-paste (use Macintoshleft arrow key)

For more details, see Copying in non-Catalyst environments

Displaying Catalyst on a PC X terminal

Introduction

Catalyst can be run on an SGI host machine and displayed on an appropriately equipped PC connected to the Ethernet network. Using X Window terminal software and an Ethernet card, the PC can provide a lower cost display terminal from which to access the full functionality of Catalyst. Catalyst runs on the PC as an X Window application, and the files are saved on the SGI host machine.

See the Notes section in the Tutorials binder for the following information about using a PC X terminal to display Catalyst:

Hardware and software requirements
Installation and configuration procedures
How to run Catalyst with a PC X terminal

Function and key differences in using a PC X terminal

Using Catalyst via an X terminal is the same as on an SGI workstation except for a few features involving the keyboard function keys and the mouse buttons, as described in this section.

Also, to copy and paste SMILES between X windows, see the section Copy and Paste Functionality on a PC.

Catalyst functions. Use the one-button mouse for Catalyst on the PC- that is, use the left mouse button and the <Shift> and <Ctrl> keys, as shown in the table.

Catalyst Function PC/ SGI Keys SGI Mouse

Select Left mouse left button

Extend Select Left mouse + Shift middle button

Rotate Left mouse + Ctrl right button

Use of mouse buttons. The PC X terminal left mouse button operates the same as on a UNIX workstation. However, the middle and right mouse buttons do not work the same. This means that in Catalyst's Help, for example, you cannot use the right mouse button to bring up the menu to access the Print command (if you want to print Help screens). Try using the F4 function key instead of the right mouse button to bring up the menu to access Print (depends upon your specific X terminal and mouse implementation).

See below for how to copy and paste text such as SMILES, which also requires using the mouse buttons differently on a PC.

Copy and paste functionality on a PC

You can copy and paste molecules in the form of SMILES between Catalyst and a PC X terminal window or a UNIX text editor on a machine running Catalyst, as shown in the two tables below. An easy way to get a molecule into Catalyst is to type or select its SMILES string in an X window, copy the string, then paste it into the View Compound workbench.

No types of objects other than SMILES strings can be cut and pasted. However, in the View Compound workbench, the SMILES string for a molecule you want to Copy is derived from its 3D structure selected in the workspace, while a SMILES string you want to Paste is expanded into its 3D structure and displayed in the workspace.

To copy SMILES strings on a PC X terminal

In this environment	Copy using this function
X terminal window	X-copy (select SMILES string with left mouse)
View Compound workbench	Copy command (Edit menu)

To paste SMILES strings on a PC X terminal

In this environment	Paste using this function
View Compound workbench	Paste command (Edit menu)
X terminal window	X-paste (use middle and right mouse buttons)

For more details, see Copying in non-Catalyst environments.

Catalyst/Hypo product description

Catalyst/Hypo has all the hypothesis-building, hypothesis-generating, conformational model generating, and activity-estimating functionality of Catalyst. Catalyst/Hypo lets you generate chemically general 3D hypotheses starting with only 2D structures and associated biological activities. You can use these hypotheses to estimate the activity of new candidates for synthesis. Catalyst/Hypo provides the following Catalyst functionality:

View Compound workbench
View Hypothesis workbench
Generate Hypothesis workbench
Estimate field in the Hit Mappings Row dialog box in the View Database workbench (requires a database server token for View Database workbench access)

The Catalyst workbenches and menu items that do not apply to hypothesis building and generation are not enabled for Catalyst/Hypo and are grayed out in the interface. For a description of the functionality offered by the full, integrated Catalyst system comprised of both Catalyst/Hypo and Catalyst/Info, see Catalyst Overview. For information on purchasing a license that provides access to all of the functionality of Catalyst, contact your MSI representative.

Catalyst/Info product description

Catalyst/Info has all the 1D-2D-3D database functionality of Catalyst. Catalyst/Info lets you build and search conformationally flexible databases, combining chemical structures, 3D geometric relationships, and property information in your hypotheses for querying databases. Catalyst/Info provides the following Catalyst functionality:

View Database workbench
Install Database and Deinstall Database commands in the Stockroom
catDB database administration and maintenance program
catSearch batch searching program

The Catalyst workbenches and menu items that do not apply to building and searching databases are not enabled for Catalyst/Info and are grayed out in the interface. For a description of the functionality offered by the full, integrated Catalyst system comprised of both Catalyst/Info and Catalyst/Hypo, see Catalyst Overview. For information on purchasing a license that provides access to all of the functionality of Catalyst, contact your MSI representative.

[Top] [Index]

Compound		A molecule with associated characteristics and descriptive information. Each Catalyst compound has a name, topology (atom connection list), stereochemical properties, and both 3D representations (one or more conformers) and 2D representations (flats). Each compound must have a unique name. A compound also has associated physical properties, such as molecular weight and biological activity. Each displayed instance can be assigned special display properties, such as color-coding of particular atoms. In Catalyst the terms molecule and compound are used interchangeably.
Database		A set of data describing a group of compounds and their properties. Catalyst can provide access to a Catalyst version of your corporate compound database. Catalyst compounds and hypotheses are saved to the StockroomDB that can be browsed and searched.
Spreadsheet		A collection of data for a set of related compounds. Spreadsheets are used to store and display the results of database searches and to store input and output data for hypothesis generation. Information can be displayed in one of several report styles. Spreadsheets can be browsed, searched, edited, printed, exported and imported.
Hypothesis		A specification of the distinguishing characteristics for a related set of compounds. Hypotheses can include topological and atomspecifications, property specifications, geometrical constraints, derived geometric objects, and high-level chemical functionality definitions. You can interactively create the significant features of a hypothesis, and then modify and use the hypothesis in other operations, such as database searches. Also, Catalyst can automatically generate a hypothesis for a set of related compounds by analyzing their structural and chemical properties and relating them to their biological activities. You can fit a hypothesis to the conformers of a sample molecule, evaluate the fit, and estimate the molecule's activity.
Workbench		A set of work areas containing Catalyst objects and commands, and workspaces in which to use them. Analogous to the workbench in a chemist's laboratory, each workbench has its shelf for materials (compounds, databases, spreadsheets, hypotheses) and its own set of tools with which to operate on the materials. Active and iconified workbenches have icons in the Stockroom or lab from which they were opened.
Lab		An object that you define and fill with compounds, databases, spreadsheets, hypotheses, and other labs related to a specific project or line of investigation. A lab is like a traditional file folder: it is the main context for organizing information.
Journal	(no icon)	A text record of the operations and Catalyst messages that occur during a session. The journal can be used to recreate a Catalyst session. The last three journals are saved automatically in separate files.

Catalyst Function	PC/ SGI Keys	SGI Mouse
Select	Left mouse	left button
Extend Select	Left mouse + Shift	middle button
Rotate	Left mouse + Ctrl	right button