Run BROOD

vBROOD runs the BROOD command-line application using a query. It can run BROOD on multiple processors, provide access to the BROOD command-line options, display the output of the command line in a log window, and display the best fragments found as the run progresses.

Loading a query

Loading a query

Loading a query

The first step to running BROOD is to load or select a query.

  • Previously build queries appear in the query list.
  • Queries can be loaded by clicking the Open item or selecting a recently loaded query from the Recents menu.
  • If the query did not have an associated protein, clicking on the Open folder in the Protein text entry will allow you to add one.

After a query is selected, it is displayed in the 3D window. Once it is loaded, clicking Next will take you to Selecting a filter.

Selecting a filter

Choose a filter

Choose a filter

A BROOD run can use a filter to limit the BROOD search and shorten the run time. vBROOD provides a built-in Druglike filter; users can also build additional filters. To use a filter, select one from the list or open a previously saved filter. See Filtering for more information on creating a filter.

To open a previously saved filter:

  • Click the Open item in the list. This will bring up a dialog that can be used to select a filter.
  • Select a filter file and click Open. This will add and select a new entry in the list.

Alternatively, you can select a filter from the Recents menu. Selecting a filter will display the filter values for the given properties in the Filter Values box below the filter list. When you are satisfied, click Next to continue to Setup BROOD.

Setup BROOD

Run options

Run options

The next step in running BROOD is choosing the run parameters. Most options correspond directly to a command-line option. Hovering with the mouse cursor over most elements in the interface provides a brief description of the option as well as the command-line flag it represents.

The multiprocessor options, found in the Quick Options section, are particularly useful. These options allow you to run multiple BROOD instances using OpenMPI on the same machine as vBROOD. This allows BROOD to make use of additional processors if they are available.

When all options are set, click Run to start the BROOD run and advance to the Run BROOD page.

Run BROOD

A run in progress A completed run
A run in progress A completed run

After Run is selected, the screen will switch to display a 2D hitlist, the BROOD Output window, and the Run Status window. This display will dynamically update as the run progresses.

  • The Hitlist shows the current cluster heads from the database.
  • The Run Status window on the left shows information about how many fragments have been processed, how many were actually scored against the query, and how many were eliminated.
  • The Output window at the bottom displays the output of the BROOD run as if it were run from the command line. This can be switched to show a spreadsheet of the top results by using the buttons on the right side of that panel.
  • At the bottom right of the vBROOD window is a progress bar and a Stop button for aborting the run.

As the run progresses, the top results are displayed in the 2D hitlist and the results spreadsheet continues to update. Both the spreadsheet and the 2D hitlist provide scrollbars for browsing the hitlist. Clicking on a 2D depiction highlights the same row in the spreadsheet and vice versa.

After a run completes, the buttons Open in VIDA and Show on Disk will be displayed and enabled. Clicking on Open in VIDA opens VIDA with the BROOD Results Viewer tool loaded (see Viewing Results in VIDA). Clicking Show on Disk opens a window displaying the directory containing the results of the run. If the run did not complete successfully, BROOD displays a dialog box and the Output window at the bottom shows the Log view. Scanning the log may provide some indication of the problem.

Click Browse Results to bring up the list of all runs for the current session. See View Results for more information.