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View Database Workbench

Tools Menu

Select a command:

Browse Databases/Spreadsheets

Fast Flexible Search Databases/Spreadsheets

Best Flexible Search Databases/Spreadsheets

Convert Molecules to Cerius2 R-Groups...

Sort by Property...

Combine Spreadsheets >

Show Selected Compounds/Mappings

Show Conformational Model...

Compute Property...

The Tools menu provides commands for browsing and searching databases and spreadsheets and for sorting the retrieved data by property. The menu also includes commands for generating R-groups for Cerius2 and for viewing retrieved compounds and their mappings to the hypothesis with which you searched the database. In addition, you can display the conformers comprising the compounds' conformational models.

Browse Databases/Spreadsheets

 The Browse Databases/Spreadsheets command lets you look at the contents of one or more databases (including the StockroomDB) and spreadsheets. Locally you can control the total number of compounds that the Browse Databases/Spreadsheets command retrieves with the value you specify in the Max Search Hits field of the View Database Options dialog box. Globally you can control this total with the value you set in the Max Search Hits field in the View Database Preferences dialog box. The local limit takes precedence over the global. For information on

Fast Flexible Search Databases/Spreadsheets

 The Fast Flexible Search Databases/Spreadsheets command uses precomputed conformations to model the flexibility of a molecule during a search. This command lets you find and retrieve compounds that match specified criteria expressed in a hypothesis. These criteria can include restrictions for

Best Flexible Search Databases/Spreadsheets

 The Best Flexible Search Databases/Spreadsheets command is the same as Fast Flexible Search Databases/Spreadsheets except that it provides a more precise database/spreadsheet search. The Best Flexible Search Databases/Spreadsheets command can modify conformations of molecules during execution and finds the best fit among those within a 20 kcal range above the global minimum. For additional information, see


Sort by Property...

 This command brings up a dialog box that allows you to reorder the entries in the report area on the basis of a selected property such as name, activity, molecular weight, and so on.

  1. Select the Sort by Property... command from the Tools menu to display the Sort By Property dialog box containing a list of properties that can be used for reordering the compounds in the report area. Use the scroll bar at the right of the list to see properties that are not visible.

  2. Click on the P symbol next to the name of the property you want, and Catalyst highlights the property name. In the Description text box, the selected property is described. The Dictionary text box identifies the property dictionary in which the property is defined. The data type (real integer, string, date, or float) is displayed in the Type text box.

  3. Select one of the Direction toggle buttons a follows: 1, 2, 3, 4... sorts entries in ascending order, and 9, 8, 7, 6... sorts entries in descending order.

  4. Select the Sort button to start sorting and leave the dialog box displayed. Select the OK button to start sorting and dismiss the dialog box. The entries in the report are reordered according to the property and direction you selected.

Best Flexible Search Databases/Spreadsheets

 The Best Flexible Search Databases/Spreadsheets command is the same as Fast Flexible Search Databases/Spreadsheets except that it provides a more precise database/spreadsheet search. The Best Flexible Search Databases/Spreadsheets command can modify conformations of molecules during execution and finds the best fit among those within a 20 kcal range above the global minimum. For additional information, see


Sort by Property...

 This command brings up a dialog box that allows you to reorder the entries in the report area on the basis of a selected property such as name, activity, molecular weight, and so on.

  1. Select the Sort by Property... command from the Tools menu to display the Sort By Property dialog box containing a list of properties that can be used for reordering the compounds in the report area. Use the scroll bar at the right of the list to see properties that are not visible.

  2. Click on the P symbol next to the name of the property you want, and Catalyst highlights the property name. In the Description text box, the selected property is described. The Dictionary text box identifies the property dictionary in which the property is defined. The data type (real integer, string, date, or float) is displayed in the Type text box.

  3. Select one of the Direction toggle buttons a follows: 1, 2, 3, 4... sorts entries in ascending order, and 9, 8, 7, 6... sorts entries in descending order.

  4. Select the Sort button to start sorting and leave the dialog box displayed. Select the OK button to start sorting and dismiss the dialog box. The entries in the report are reordered according to the property and direction you selected.

Convert Molecules to Cerius2
R-Groups...

 The Convert Molecules to Cerius2 R-Groups command lets you create a series of R-groups (fragment molecules) from a hypothesis and a spreadsheet.

In combinatorial chemistry, one of the procedures is to create a library of molecules by attaching sets of R-groups to a core molecule. In Cerius2, combinatorial library creation is made possible by the Analog Builder module.

Catalyst search tools allow you to search databases for molecules containing specific functional groups such as esters, primary amines, etc., and Catalyst's Convert Molecules to Cerius2 R-Groups command allows you to convert the molecules resulting from the search into R-groups that can be placed into the Cerius2 fragment directory for use in the Cerius2 Analog Builder. The R-groups are written out in .msi format to individual files.

To use the command:

  1. Create a hypothesis that is a fragment of a molecule.

    Hypotheses containing chemical functions (such as HB donors, hydrophobes, etc.) are not suitable for this.

    For more information about building hypotheses see:

  2. Search a database for molecules satisfying the hypothesis query using the Best Flexible Search Databases/Spreadsheets command or the Fast Flexible Search Databases/Spreadsheets command described above.

  3. Use the Save Report to Lab As Spreadsheet command on the Data menu to save the search report as a spreadsheet.

  4. Extend select both the spreadsheet and the hypothesis on the shelf of the View Database workbench.

  5. Select the Convert Molecules to Cerius2 R-Groups command from the Tools menu. This opens the Convert Molecules to Cerius2 R-Groups dialog box.

  6. The hypothesis is shown in the graphic display area of the dialog box. Extend select an atom and an adjacent bond. The atom is the linkage atom and the bond is the cleavage bond. When the command is issued, each R-group fragment is created by deleting all atoms connected to the linkage atom except for those that are on the other side of the cleavage bond. The linkage atom is replaced by X in the output file. Note also that the cleavage bond should not be in a ring.

  7. If the directory name specified in the Output Pathname field is not suitable, edit this field. The specified directory will be created if it does not already exist. If the directory already exists, a warning will be issued.

  8. Choose the OK button to execute the command. For each molecule in the spreadsheet a .msi file is written to the Output Pathname directory.

  9. Choose the Cancel button to close the Convert Molecules to Cerius2 R-Groups dialog box.

Combine Spreadsheets > In First AND In Second

 The In First AND In Second option for the Combine Spreadsheets command compares two spreadsheets and produces a local spreadsheet in the report area containing only the compounds that

You can use this command to create a local spreadsheet consisting only of the compounds that are duplicated in the two spreadsheets being compared with the Combine Spreadsheets command. The local spreadsheet contains the union of all the 1D properties in the two source spreadsheets and their up-to-date associated 1D property data. Duplicated compounds with "dirty" data from source spreadsheets do not appear in the resulting local spreadsheet. To qualify as matching compounds, molecules must have the same name and same internal compound reference number (cref), and they must reside in the same database from which the source spreadsheets were derived. Compounds with the same structures from the same database, but with different names and crefs do not meet this criterion.

To use the command:

  1. Extend select the two spreadsheets you want to compare.

  2. Select the Combine Spreadsheets command from the Tools menu to display the submenu.

  3. Click on the In First AND In Second option in the submenu. Catalyst displays a local spreadsheet in the report area containing all compounds that occur in both of the source spreadsheets you selected. If no compounds occur in both source spreadsheets, Catalyst displays a message advising you that no compounds meet the command criteria.

Combine Spreadsheets > In First OR In Second

 The In First OR In Second option for the Combine Spreadsheets command compares two spreadsheets and produces a local spreadsheet in the report area containing the compounds that occur in each of the source spreadsheets. You can use this command to create a local spreadsheet consisting of the union of compounds in the two spreadsheets being compared with the Combine Spreadsheets command.

Up-to-date associated 1D property data and "dirty" (not yet committed to the database and therefore in gray cells) data for each compound in the source spreadsheets are handled as follows in the resulting local spreadsheet:

Rows in tabular style source spreadsheets

 Rows in tabular style local spreadsheet

1 up-to-date and 1 dirty

 1 dirty

1 up-to-date and 1 up-to-date

 1 up-to-date

2 dirty

 2 dirty

To arrange compounds in the resulting local spreadsheet alphabetically by name, use the Sort by Property... command on the Tools menu. This is particularly handy when a compound has two sets of dirty data; alphabetizing puts them next to each other in the report.

Note: To qualify as matching compounds, molecules must have the same name and same internal compound reference number (cref), and they must reside in the same database from which the source spreadsheets were derived. Compounds with the same structures from the same database, but with different names and crefs do not meet this criterion.

To use the command:

  1. Extend select the two spreadsheets you want to combine.

  2. Select the Combine Spreadsheets command from the Tools menu to display the submenu.

  3. Click on the In First OR In Second option in the submenu. Catalyst displays a local spreadsheet in the report area containing all compounds that occur in each of the source spreadsheets you selected.

Combine Spreadsheets > In First but NOT In Second

 The In First but NOT In Second option for the Combine Spreadsheets command compares two spreadsheets and produces a local spreadsheet in the report area containing only the compounds that

For example, if you have two spreadsheets, the first of which has the same three compounds that also occur in the second spreadsheet, you can use this command to create a local spreadsheet consisting of the first spreadsheet's compounds minus the three that are duplicated in the second spreadsheet. A duplicate is the same compound with the same name and internal compound reference number (cref) residing in the same database from which the source spreadsheets were derived. Compounds with the same structures from the same database, but with different names and crefs, do not match this criterion.

The local spreadsheet contains the 1D properties in the first source spreadsheet selected and the up-to-date associated 1D property data for those compounds occurring in the first source spreadsheet and not in the second. The local spreadsheet also contains any other compounds in the first source spreadsheet with "dirty" data.

To use the command:

  1. Extend select the two spreadsheets you want to compare. The order in which you select source spreadsheets affects the resulting local spreadsheet.

  2. Select the Combine Spreadsheets command from the Tools menu to display the submenu.

  3. Click on the In First but NOT In Second option in the submenu. Catalyst displays a local spreadsheet in the report area containing all compounds in the first source spreadsheet and not in the second plus any others in the first spreadsheet that have dirty data. If there are no compounds that meet these criteria, Catalyst displays a message to that effect.

Show Selected Compounds/Mappings

 The Show Selected Compounds/Mappings command lets you display a compound from the report area in the 3D workspace of the Hit Mappings Row dialog box. There you can rotate, move, and resize it as you can in any 3D workspace. The command also displays, in a dotted style, the parts of a hit compound that match the hypothesis if a search generated the compounds in the report area. For detailed information on how to use this command, see "Displaying Hit Compounds."

Show Conformational Model...

The Show Conformational Model... command provides a dialog box with a 3D workspace to view and manipulate a set of conformers representing the conformational model for a compound. You can look at the conformers by stepping through them one at a time, or optionally, Catalyst will step through them automatically. This command is the same in all workbenches.

For more information, see "To Display, Delete, Register, and Unregister Individual Conformers."


Compute Property...

For compounds in a spreadsheet, the Compute Property... command lets you calculate values for the following properties defined in the property dictionary file $CATALYST_CONF/Biocad.bpd:

For the step-by-step procedure for using the Compute Property... command, see "Displaying Computed Property Data".

ReportStyle Menu

Select a command:

2D3D-Compound

BioByte

Compound-All

Compound-Table

Four-per-page

Six-per-page

Structure-Activity-24

Structure-Activity-9

Structure-Activity-View

Structure-View-12

The ReportStyle menu provides different formats for displaying and printing spreadsheet data.


2D3D-Compound

The 2D3D-Compound report style shows data for two compounds per printed page. In its default state the format includes areas for a 2D and 3D drawing of each compound as well as for values for each of the following properties: Name, MW, Formula, CAS, Activity, and Estimate.


BioByte

BioByte is intended for use with the BioByteMasterFile database, and it resembles Compound-Table, the default report style for this workbench. The report style shows 1D property data for 30 compounds per printed page. In its default state the format includes areas for values for each of the following properties: Name, MW, Activity, LogP, CASnumber, pKa, and Remarks.


Compound-All

The Compound-All report style shows data for one compound per printed page. In its default state the format includes areas for a 2D and 3D drawing of each compound as well as for values for all 1D properties.


Compound-Table

Compound-Table is the default report style for this workbench. It shows 1D property data for 30 compounds per printed page. In its default state the format includes areas for values for each of the following properties: Name, MW, Formula, Activ, CAS_num, Chemist, and Activity_1.


Four-per-page

The Four-per-page report style shows data for four compounds per printed page. The format includes areas for a 2D drawing of each compound as well as for values for each of the following properties: CAS, MW, Formula, and Name.


Six-per-page

The Six-per-page report style shows data for six compounds per printed page. The format includes areas for a 2D drawing of each compound as well as for values for each of the following properties: CAS, MW, Formula, and Name.


Structure-Activity-24

The Structure-Activity-24 report style shows data for 24 compounds per printed page. In its default state the format includes areas for a 2D drawing of each compound as well as for values for the compound name and Act.


Structure-Activity-9

The Structure-Activity-9 report style shows data for 9 compounds per printed page. In its default state the format includes areas for a 2D drawing of each compound as well as for values for the properties, Name and Act.


Structure-Activity-View

The Structure-Activity-View report style is intended for displaying compounds on your monitor; it is not intended for printing. In its default state the format shows data for 9 compounds per page, and it includes areas for a 2D drawing of each compound as well as for values for the properties, Name and Act.


Structure-View-12

The Structure-View-12 report style is intended for displaying compounds on your monitor; it is not intended for printing. The format shows data for 12 compounds per page, and it includes areas for a 2D drawing of each compound as well as for values for the Name property.


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Last updated April 17, 1996 at 12:21pm PDT.
Copyright © 1999, Molecular Simulations Inc. All rights reserved.