Query Cambridge Structural Database Panel

Send a query to Mogul for a set of ligand molecules, to obtain a report on the match between the geometric parameters of the molecules and those found in the Cambridge Structural Database (CSD).

To open this panel: click the Tasks button and browse to Structure Analysis → CSD Search.

  • Using
  • Features
  • Additional Resources

Using the Query Cambridge Structural Database Panel

To use this panel, you must have an installation of Mogul that is configured for use with Maestro. See Configuring Mogul for Maestro Use for instructions.

Query Cambridge Structural Database Panel Features

Query CSD with ligands from option menu

Choose the source of the ligands to send as queries to the CSD.

  • Project Table (selected entries)—Use the entries that are selected in the Project Table. When you select this option, the number of ligands selected is reported below.

  • Workspace—Choose the query ligands from the structures in the Workspace. The ligands in the Workspace are automatically detected and listed below, under Select a ligand from the list.

Select a ligand from the list list

List of ligands in the Workspace. You can select multiple ligands from this list to use as queries.

Search fragments options

Select options for the geometric parameters you want to obtain reports on for the query ligands.

  • All torsions—report on the torsional angles around bonds
  • All angles—report on all the bond angles
  • All bonds—report on the lengths of all the bonds
Filters button

Filter the structures in the CSD that are used to create a report on the query structures. Opens the Filters dialog box, in which you can select one of the following options to apply a filter, and choose a filter value from the option menu.

  • R-factor—include only molecules with an R-factor less than the specified percentage. Choose the percentage range from the option menu.
  • Exclude—exclude solvent molecules or non-solvent molecules, by choosing from the option menu.
  • Heaviest element—exclude molecules containing elements heavier than that selected from the option menu.
  • Exclude—exclude organic molecules or organometallic molecules, by choosing from the option menu.
Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Query Cambridge Structural Database - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

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