Manage Phase Database Panel

In this panel you can manage a Phase 3D database, by adding, deleting, or exporting structures and creating and deleting subsets.

To open this panel, do one of the following:

  • Click the Tasks button and browse to Ligand-Based Virtual Screening → Manage Database
  • Click the Tasks button and browse to Structure Analysis → Manage Phase Database
  • Click the Tasks button and browse to Ligand Preparation and Library Design → Manage Phase Database
  • Click the Tasks button and browse to Phase → Manage Database

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see phase_database Command Help and Managing Databases with phase_database.

  • Features
  • Additional Resources

Manage Phase Database Panel Features

Open database text box and Browse button

Enter the name of the database to use in this text box, or click Browse and navigate to the database. If the database is in the current format (.phdb) it is opened and read.

If the database is in an earlier format, (e.g. its name ends in _phasedb), the Phase Database Converter panel opens, and you can click Convert to convert the database. The status is indicated in the panel. When the conversion finishes, a dialog box opens to ask if you want to open the database.

New button

Create a new, empty database. Opens a file selector, in which you can navigate to the location for the database and name the database.

Structures table

This table lists the structures in the database, subject to the conditions set in the Show structures section. The table includes properties of the structures. Each row represents a molecule, which can be included as a single structure or as a set of conformers. The number of structures is indicated in the #Confs column. The Site column indicates whether sites have been generated for the molecule. Other columns include the molecule ID and the title.

Add button

Add structures to the database. Opens a file selector, in which you can select a structure file. When you click Open, a dialog box opens asking you if the file contains conformer sets. After responding, the file is used as input to a phase_database import job, which adds the structures to the database.

Delete button

Delete structures from the database. When you confirm the deletion, a phase_database delete job is run to delete the structures.

Update button

Update the properties shown in the table. Runs a phase_database extract job to update the properties.

Select All button

Select all the structures in the table.

Select by Titles button

Select structures by matching the titles with a list of titles read from a file. Opens a file selector, in which you can navigate to and open the file that lists the titles, one per line.

Export button

Export the selected structures to a Maestro (.maegz) or SD (.sdf) file. Opens a dialog box, in which you can choose to export all conformers or only the first conformer for each molecule. When you click OK, a file selector opens, in which you can choose the format, navigate to the location, and name the file.

Add to Project Table button

Add the selected structures to the current Maestro project as project entries.

Show structures section

This section provides tools for limiting the number of structures that are shown in the Structures table. For large databases, showing many structures can make panel operations slow. Selecting a subset in the Subsets section shows all the structures in the subset by default, and hides all other structures. You can then filter the structures in the subset with the tools in this section.

All button

Show all structures that are in the database.

Selected button

Show only the structures that are selected in the table.

IDs text boxes

Show only the structures in the range of structure IDs specified in the text boxes, after clicking Apply.

Titles text box

Show only the structures whose title matches the string in the text box. You can use the SQL wildcard character % to match an arbitrary string. For example, the string %mol_10% will match the titles mol_101, mol_102, mol_1034, newmol_100, etc. To filter the structures, click Apply. If you have a subset selected, the filter applies to the subset, and shows only structures that match within the subset.

Apply button

Click this button to show only the specified structure range or the structures with the specified titles.

Subsets section

In this section you can create database subsets. These subsets are stored as subset files, ending in _phase.inp.

Subset table

This table lists the subsets by name. The name is the file name without the _phase.inp extension.

New button

Create a new subset from the selected structures or from a random selection of the structures. This button opens the Manage Phase DB - New Subset dialog box, in which you can name the subset and select the structure source. If you select Random, you can specify the size of the subset (number of structures) and a seed for the random number generation. If you select File, you must specify a subset file, either by entering the name in the text box, or clicking Browse and navigating to the file.

When you click OK, the subset file is created, by appending the extension _phase.inp to the subset name.

Delete button

Delete the selected subsets.

Clear button

Deselect all the selected subsets (clear the selection).

Reset button

Clear all data in the panel, except for the database name. This action effectively "closes" the database. To manage another database (or the same database), you must open it.

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