Menus in All Workbenches

Data menu

• Open
• Save To Lab As
• Save As Local Object
• Save Report To Lab As Spreadsheet
• Commit 1D Changes To Database
• Print
• Import
• Export
• Export Workbench Alignments
• Find
• Dispose from Workbench

Several menu items are available only in certain workbenches.

Open

Object selected	Workbench opened
No object	View Compound
Compound	View Compound
Hypothesis	View Hypothesis
Database	View Database
Spreadsheet	View Database

In a lab or the Stockroom, if a lab is selected, the Data/Open menu item opens the lab. If an iconified workbench is selected, that workbench opens. If the selected lab or workbench is already open, it pops to the top of the windows displayed on screen (if it was hidden previously, it will be visible now).

You also can double-click an object to open the appropriate workbench, instead of using the Data/Open menu item.

Save To Lab As

When you save a compound to the shelf, these properties are saved:

• Selected independent fragments or multicomponent compounds (salts), as long as each fragment has the proper valence and the aggregate charge of all multicomponent compounds is zero.
• All registered and unregistered conformers, including the edit conformer.
• The display orientation of the molecule.
• 2D representations (flats) for the compound.

You cannot save a compound to the same name if its topology has been modified, since it is then considered to be a new molecule. If any of the following attributes have been changed, but not the topology, the compound is considered to be revised and can be saved with the same name:

• A new flat can be added if only the 2D geometry is different.
• The edit conformer can be replaced if its geometry has been altered.
• The 3D orientation can be replaced.
  

When you save a hypothesis to the shelf, these properties are saved:

• Selected independent hypotheses, topology specifications, and functions.
• The orientation of the hypothesis.
• The 2D representation for the hypothesis.

When you exit Catalyst, you can choose to save the StockroomDB, which saves all objects in the Stockroom and in all labs and also saves the global and workbench preference settings. Then the next time you start Catalyst, the Stockroom contains all the objects it contained the last time that you saved the StockroomDB.

For more details about saving objects, see To save an object to the shelf of a lab.

Save As a Local Object

A local object on a workbench shelf has the same appearance as a saved object, except that the identifying object symbol on the icon has an L in the center, and its name is of the form Local-n, where the number n distinguishes multiple local objects of the same type on the shelf. A local object cannot be dragged and dropped to any other workbench or lab, but it can be dropped into a QuickTool associated with the workbench. The local object can be renamed by clicking the text around the icon, editing the text, and pressing the <Enter> or <Return> key.

To change a local object to a regular 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. See Save To Lab As for additional information.

Save Report To Lab As Spreadsheet

When you save an object to the shelf, Catalyst allows you to specify a lab (via the Lab control in the Save Report To Lab As Spreadsheet control panel) in which to save the object. The default is the lab in which the workbench was opened; if you did not open the workbench in a lab, the default is the Stockroom. Catalyst saves the object to the specified lab, in addition to saving it to the shelf in the current workbench.

When you exit Catalyst, you can choose to save the StockroomDB, which contains everything in the Stockroom and in all labs. The next time you start Catalyst, the Stockroom contains all the objects it contained the last time that you saved the StockroomDB.

Commit 1D Changes To Database

In the View Database workbench, the Commit 1D Changes To Database menu item appears in the Databases menu.

Print

• Print the image displayed in a workspace of any workbench to a color or black-and-white printer.
• Save the image displayed in a workspace as a PostScript file.
• Print the contents of a report in the View Database or Generate Hypothesis workbench to a color or black-and-white printer.
• Save the contents of a report in the View Database or Generate Hypothesis workbenches as a PostScript file.

• To print the results of a search
• How to fill in the Print control panel

Printing the contents of a workspace

The Objects option produces a printout at the resolution of your printer, but the image is flat-shaded. That is, shading is not smooth and spheres appear faceted on the printed page. The background is white, and any text (such as atom labels or compound names) is black. Text prints clearly, and the pan and zoom widgets do not appear in the printed copy. The Objects option usually gives a sharper and better image, although it does not look exactly like the image on the screen. The Objects option also produces the best results when printing the contents of the 2D workspace. Here is a molecule printed with the Objects option:

The Print menu item also allows you to save the image in a workspace as a PostScript file, as a PostScript file containing a raster image, or as an encapsulated PostScript file. This is useful if you want to print an image or a report again or if you want to import it into another application, such as a graphics, desktop publishing, or word-processing program. You can send a saved PostScript file to a printer directly with the UNIX lp or lpr command.

You can send a report in the View Database or Generate Hypothesis workbench to a PostScript file or to a black-and-white or color PostScript printer. How your report is formatted depends on the style you select from the ReportStyle menu in the View Database workbench. For detailed information on report styles, see ReportStyle menu.

How to fill in the Print control panel:

1. Select the Data/Print menu item to open the Print control panel:
   
2. Make your selections from the controls in the panel:
   • Print From
     • Workspace - print the contents of a Catalyst workspace. If your workbench has two workspaces, assure that the correct one is selected by clicking the Select 2D or Select 3D tool in the toolbox.
     • Report - print the contents of a report.
   • Print Scene As
   • Objects - print the individual objects in the scene with full PostScript resolution.
   • Screen Dump - print the images as they appear on the computer display.
   • Pages
   • All - print the entire report.
   • First - enter the First and Last page numbers to print part of a report.
   • Copies - number of copies of the printout.
   • Border
   • On - draw a black rectangular border around the printout of the graphics area.
   • Off - no border. (Always off for printing reports.)
   • Destination
   • Printer - print now. Enter the UNIX command and name of a color or black-and-white PostScript printer that you can print to.
     If you do not know a valid printer name, see your system administrator.
   • File - store as a PostScript file. Enter only a filename if the file is to be saved in the current directory or a full UNIX path preceding the filename if it is to be saved in a different directory. To send your displayed data to an encapsulated PostScript file that you can later import into a graphics or word-processing application, select both File and EPS.
     Catalyst does not automatically supply a filename suffix such as .eps or .epsi. Thus, if the application into which you plan to import the file requires a particular filename suffix, you should include it when you enter the filename.
3. After filling in the control panel, select the Print button. Catalyst grays out the control panel while processing the printing specifications and then closes the control panel. If you are sending report data to a file, the data are copied and saved in the file immediately. If the file to which you are sending data already exists, an alert box asks you to confirm that you want to overwrite the file.

Import

• To import objects one at a time
• To import multiple objects

Export

Before you can export an object you must save it to the shelf.

The formats available for exporting objects are:

Molecules

Molecule description files in standard SMILES, MOL, HIN, SKC, MOL2, and MMOD formats or in Catalyst formats CPD and TPL.

Hypotheses

Hypothesis description files in Catalyst CHM or MDL MOL format.

Spreadsheets

Spreadsheet description files in Catalyst SPST format, extended database spreadsheet description files in Catalyst ESP format, or MDL structure-data files.

Export Workbench Alignments

To use the Export Workbench Alignments menu item:

1. To map compounds to a hypothesis, follow the steps outlined in Show selected compounds or mappings.
2. After Catalyst displays the compounds mapped to the hypothesis, select the menu/Export Workbench Alignments menu item to open the Export Alignment control panel:
   
3. Under Export Alignment as, choose the type of file to export (SYBYL molecule file (MOL2) or Database structure-data file (SD)).
4. By default, the Directory popup shows the name of the currently selected directory as the target directory for the file you're exporting. Names of the subdirectories of the current directory are shown in the Directory list box. To select a subdirectory as a target, click its name. Catalyst now shows the name of the selected subdirectory on the Directory popup.
   To select a directory that is above the current directory in the file hierarchy, click Directory popup and choose a directory name from the popup menu.
   To select a directory that you have visited before in this Catalyst session, use the Previous Directories popup.
5. Click in the File Name box and enter a name for the file you're exporting. It can be useful to include a period and an extension (.sd or .mol2) reflecting the type of file you specified in Step 3.
6. To save the file to disk in the directory you've specified, click Export. Catalyst exports the file containing the selected compounds in precisely their orientation in the workspace and closes the Export Alignment control panel. The hypothesis is not exported. You can now use the aligned compounds in other products that accept .sd or .mol2 files.

Find

For information on creating a 1D hypothesis with which you can search databases and spreadsheets for property (1D) data that includes a compound's name, molecular weight, and other defined properties see To specify searching criteria for 1D property data.

When the search started by the Find menu item is complete, the number of objects found is reported in the control panel, and the name of the first object found is displayed in the Object Name box. You can save any compounds found in a database to the shelf or copy a compound found in the StockroomDB to the shelf (the original compound is already in the StockroomDB).

To find an object according to its name:

1. Select the Data/Find menu item to open the Catalyst: FIND control panel:
   
2. Under Search in, extend-select the databases you want to search.
3. Under Look for, select Compounds, Hypotheses, Spreadsheets, and/or Labs to select the types of objects you want to locate. When you select types other than Compounds, searching is restricted to the StockroomDB.
4. Enter the full or partial name of the object(s) you want to find in the Find item entry box. The search is not case sensitive, so you can include any combination of upper- and lower-case letters in the name.
   You can use a % (percent character) as a wildcard (which stands for any string of characters). For example, entering c%e in the Find item entry box means to search for all objects with a name that begins with c and ends with e when you have Substring selected under Match. That is, Catalyst matches the pattern you specify when you include the % character in the character string you specify for a Substring search. Specifying a Substring search for a character string that does not contain a % character has the effect of putting a % at both the beginning and end of the string for which you're searching.
5. Choose Substring or Exact as the type of Match you want to apply during the search. Substring specifies implied wildcard characters preceding and following the string you enter in the Find item entry box (unless you explicitly include wildcard characters, in which case no more wildcards are added). Therefore, if you want to search for all compounds with phenyl in their names, for example, you need only enter phenyl. To treat the character string you enter in the Find item entry box as a whole word and locate only those objects with names that precisely match it, select Exact.
6. Click the Find button at the bottom of the control panel to start searching. Catalyst displays a Busy box to show you the progress of the search. If you want to halt the process before it completes, click the Stop button.
7. Catalyst displays an Alert box advising you if no objects match your search criteria or if the number of objects located exceeds the current value for Max Find Hits (set with the Preferences/Global Preferences menu item). Otherwise, at the end of the search Catalyst shows the name of the first object to match your search specification in the Object Name box in the Catalyst: FIND control panel. The name of the database in which the object resides is shown in In DB box; for example, Stockroom/Test44 means that the object is in a lab called Test44 in the StockroomDB. The Type box shows Compound, Hypothesis, Spreadsheet, or Lab. The Number box shows 1 of n, where n is the total number of objects found. For example, if 28 compounds matched your search string, the Number box displays 1 of 28.
8. To step through the names of the objects found, use the controls near the bottom of the control panel:
   
   • Slider - drag the slider to the right to select an object toward the end of the list of found objects and to the left to select an object toward the beginning of the list of found objects. The object's number appears above the slider and in the Number box.
   • Fast Reverse - step backwards through the names of objects found.
   • Stop - stop the action of the Fast Forward or Fast Reverse button.
   • Fast Forward - step forward through the names of objects found.
9. The functions of the buttons at the bottom of the control panel are:
   • Show - open the FIND SHOW window in which Catalyst displays the 2D topology of a compound or 3D features of a hypothesis.
   • Save to Shelf - edit or analyze a compound found in a database other than the StockroomDB. The compound is copied from the database into your Stockroom and its icon is placed on the workbench shelf.
   • Sample to Shelf (name of the Save to Shelf button when a compound is found in the StockroomDB) - copy the compound to the current workbench (the original compound remains in the Stockroom or lab in which it was found).
   • Open Lab (appears when the found object is a lab) - open the lab.
   • Cancel - close the control panel.
10. If you want to do more searches, enter a new character string, and wildcard characters if needed, and repeat the process.
11. When you are finished searching for and saving the compounds you need, select Cancel to close the control panel.

Dispose from Workbench

To use dispose of objects, first select the relevant objects from the shelf and then select the Data/Dispose from Workbench menu item. The objects disappear from the shelf.

If the Dispose from StockroomDB menu item is used on selected objects in a lab or the Stockroom, the objects are removed from your Catalyst session, including from any workbench that contained copies of them.

Edit menu

• Copy
• Paste
• Select All
• Duplicate
• Clear Display
• Clear Selected Report Rows
• Clear All Report Rows
• Create/Edit Hypothesis 1D Properties
• Clear Current Hypothesis
• Set Current Hypothesis
• Selection Options

For workbenches with tabular reports, the Edit menu includes several items for modifying entries, spreadsheets, and hypothesis properties.

Some menu items are available only in certain workbenches.

Copy

To use the Copy menu item, select some part of each of the desired substructures to be copied, then select the Copy menu item (no visual feedback occurs). After copying the substructure, you can paste its SMILES string into any of the following:

• As a text string into any Macintosh application running along with Catalyst under MacX X-terminal software.
• As a text string into an editor such as vi or emacs on a UNIX workstation.
• As a substructure into a Catalyst workspace. This is useful if you want to duplicate unsaved topologies that are displayed in the workspace.
• Into an X-terminal window.

Copying in non-Catalyst environments

1. Assure that an X-terminal window running the application you want to copy from is open on your machine.
2. In the X-terminal window or the Macintosh application, type or display the required SMILES string.
   
3. Select the text of the SMILES string.
   If the SMILES string is in an X-terminal window, select it by pressing the left mouse button down at the start of the text and keep the button pressed down while you drag the cursor across the SMILES string to highlight it.
   
   If you are copying the SMILES string from a Macintosh application, select the text in the usual way for the application, then select the Copy menu item in the application to copy the SMILES text string to the clipboard. (In ChemDraw Plus, use the Copy SMILES menu item.)
4. Paste the SMILES string into Catalyst as described under Paste menu item.

Paste

1. To use the Paste menu item, first copy the SMILES string for the desired structure into the clipboard in one of the following ways:
   • Using the Catalyst Copy menu item (see above).
   • Using the Macintosh Copy menu item in a word processing application or the ChemDraw Plus Copy SMILES menu item (applications running, along with Catalyst, under MacX X-terminal software).
   • Using the UNIX cp command in an X-terminal window.
   For copying from other environments, see Copying in non-Catalyst environments.
   
2. In the View Compound workbench in which you want to paste the structure, select the Edit/Paste menu item.
   The structure is displayed in the View Compound workspace.

Select All

For a lab, the menu item selects all icons on the shelf.

For the View Database workbench, the menu item selects all occupied rows of the report.

Duplicate

To use the Duplicate menu item:

1. Select the atoms and bonds you want to duplicate:
   
2. Select the Edit/Duplicate menu item. (Duplicate will appear as the current selection in the Periodic Table.)
   
3. Click in the 2D workspace. A new group appears, consisting of the duplicated selection, with additional hydrogens to make it a chemically correct molecule. (The additional hydrogens do not appear in the 2D workspace unless you have View/Hydrogens switched on for the 2D workspace.)
4. The newly added duplicate is not physically connected to the original molecule, although it is part of it. (If you try to move either the original molecule or the newly added duplicate you see that they both move together, indicating they are part of the same object.) You can physically connect them if you want, by selecting one of the atoms in the duplicate entity in the 2D workspace and then clicking the atom in the original molecule that you want to connect it to.

An example of the use of Duplicate:

Clear Display

Clear Selected Report Rows

Clear All Report Rows

Create/Edit Hypothesis 1D Properties

For detailed information on how to use the Create/Edit Hypothesis 1D Properties menu item, see To specify searching criteria for 1D property data.

Clear Current Hypothesis

Set Current Hypothesis

You also can drag the hypothesis and drop it into the Current Hypothesis text box. Its name is displayed there and it becomes the current hypothesis.

Selection Options

You can select the objects to be changed before selecting the menu item or while the Set Options On Selections control panel is open. The changes take effect only on objects that are selected when the changes are applied.

To specify a 3D display style for selected objects

1. Select the object or objects in the 3D workspace that you want to display differently.
2. Select the Selection Options menu item. The Set Options on Selections control panel appears and allows you:
   • To set colors for a selection.
   • To set 3D rendering styles for selected objects (molecules, constraints, and geometric objects).
   • To set 2D/3D viewing attributes for a selection.

To set 3D rendering styles for selected objects

• 3D Style - choose the molecule or hypothesis topology display styles Wireframe, Mesh, Dots, Tube, Ball and Tube, Sphere and Rod, or Spacefilling.
• 3D Constraint Style - choose the hypothesis constraint-display styles Invisible, Mesh, Dots, Transparent, or Solid.
• 3D Geometric Object Style - choose the geometric object styles Invisible, Mesh, Dots, Transparent, or Solid.

To set 3D rendering styles, with the Set Options on Selections control panel displayed:

1. In the 3D Rendering section, click the style type you want to change. A popup menu appears.
2. Choose the style you want. You can apply different styles to different parts of a molecule or hypothesis fragment.
3. Select OK to apply the changes and close the control panel.
   Select Apply to apply the changes and leave the control panel on the screen.
   Select Reset to return all values to their original values.
   Select Cancel to close the control panel without making any further changes.

To set 2D/3D viewing attributes for a selection

Select OK to apply the changes and close the control panel.
Select Apply to apply the changes while leaving the control panel on the screen.
Select Reset to return all values to their original values.
Select Cancel to close the control panel without making any further changes.

To set colors for a selection

1. In the workspace, select the objects whose colors you want to change.
2. In the Set Options on Selections control panel, click the Set Color toggle:.
   
3. Select the Selection Color button. The color wheel control panel appears.
   
   You can use the color wheel control panel to experiment with the color you want before applying it to selected objects in the workspace. You can use controls for hue (color), saturation (intensity), and brightness, as well as percent red, green, and blue. The combination of these variables represents a 3D wheel of color selections.
4. Experiment with the various controls and observe the resulting change in the selected color. The selected color marker (+) moves on the wheel as the sliders are adjusted, and the color in the color sample box changes color accordingly. The individual parameter adjustments are described below.
   • Hue - pick the hue and intensity you want directly by clicking the desired color on the color wheel.
     Or you can drag the Hue slider between 0 and 360 degrees (representing the angle on the wheel), changing the color at constant saturation and brightness values.
   • Saturation - drag the Saturation slider between .00 (minimum) and 1.00 (maximum) at constant hue and brightness values. Higher saturation represents less gray and therefore more intense color.
   • Brightness Value - drag the Brightness Value slider between .00 (black) and 1.00 (maximum brightness for the given color).
     Or click the brightness value from the vertical brightness value scale.
   • Red, Green, Blue balance - choose the color by choosing the individual fractions of red, green, and blue with the sliders.
5. When you have the desired new color displayed in the new color box (bottom left), select Ok. The color wheel control panel is closed, and the new color is reflected in the color box in the Set Options on Selections control panel.
   If you select Cancel, the color wheel control panel is closed without selecting a new color.
6. Click the Apply button to apply the new color to the selected objects.
   Or, if you select Restore Color and then Apply, the colors of the selected object are returned to their defaults.
7. The other control panel buttons have the following functions:
   • OK - apply the changes and close the control panel.
   • Reset - return the values in the control panel to what they were when the control panel opened (does not change anything in the workspace).
   • Cancel - close the control panel without making any further changes.

Workbench menu

• Tidy Shelf
• View As
• Workbench Options
• Workbench Layout
• Iconify Workbench
• Dispose of Workbench

Tidy Shelf

• By Object Name (alphabetically).
• By Object Type, to sort so that databases are shown in the top row starting with the StockroomDB, followed by labs, compounds, hypotheses, and spreadsheets.
• By Object Location, to leave icons in the same sequence.

View As

Icons: Display all shelf objects as approximately square icons.

Small Icons: Display all shelf objects as small approximately square icons.

Names: Display all shelf objects as rectangles labeled with the object's name (default).

Workbench Options

More information on customizable features:

• View Compound and View Hypothesis workbenches
• View Database workbenches
• Generate Hypothesis workbenches

View Compound and View Hypothesis workbenches

• 2D and 3D Background Colors. Set the background colors by choosing the 2D Background or 3D Background buttons. A color wheel is displayed allowing you to select the background color you want. For more details, see To set colors using the color wheel control panel.
• 2D Attributes. Set parameters such as grid snap, grid spacing distance, square and hexagonal grid patterns, and maximum rubber band length. For more details, see 2D attributes.

View Database workbenches

• Maximum Search Hits - set the maximum number of hits in a database search. The search terminates when it reaches the maximum setting.

Generate Hypothesis workbenches

• Workspace Colors. You can set 3D background colors using the color wheel control. For more details, see To set colors using the color wheel control panel.
• Overlay Controls. You can display compounds with special distinguishing colors for Compare/Fit using the Overlay Controls section of the control panel. The available controls are:
  • Apply Color To set which atoms have special colors applied.
  • All Atoms display all atoms and bonds in the selected color.
  • Only Non-Heteroatoms display heteroatoms in normal 3D colors.
  • No Atoms display all atoms in their normal 3D display colors.
  • Colorization set the special colors to be used in quick Compare/Fit.
  • Spectrum use the compound color from the tabular report (Color column) to color atoms and bonds.
  • Binary use colors from the active/inactive color specifications.
  • Activity Threshold set the activity value below which compounds have the special color assigned to active compounds, and above which compounds have the special color assigned to inactive compounds.
  • Actives/Inactives open a control panel to set a unique color to display active and inactive compounds (as determined by the Activity Threshold). The color boxes next to the buttons show the present settings for the active and inactive colors.

Workbench Layout

Iconify Workbench

To open an iconified workbench, select the workbench icon in the Stockroom and select the Data/Open menu item.

Dispose of Workbench

Copies of saved objects contained in the disposed workbench also are lost, but the original objects remain in the Stockroom or lab to which they were saved. Any open control panels associated with the workbench are closed, and any unapplied changes are lost.