BioResource Navigator

The View

The BioResource Navigator is the most important view in Bioclipse as it displays all BioResources available in the selected directories. The topmost folder is called the Base Folder, and is likely a folder on your local hard disk that contain BioResources e.g. molecules, spectra, sequences etc. For setting the Base Folder, right click within the BioResource Navigator and select "Set new base folder".

[Image: Select new base folder]

Double-clicking
This parses the BioResource and opens up the default selected editor. This is the same as applying the "Open" action described below.

Single-clicking
Single-clicking, also called selecting, a BioResource does not load and parse it but just shows the file properties in the Properties View. Stepping with the keyboard

Actions

New...
This action allows for the creation of new BioResources using one of the available Wizards. Most wizards are contributed by plugins, but the standard set includes:

Open
This opens the BioResource with the default registered editor. This is the same action as achieved by double-clicking the BioResource.

Open...
This action allows the user to select which editor he'd like to open the selected BioResource in. Only editors compatible with the BioResource are shown.

Set Base Folder
This allows the user to select a new “Base Folder”.

Delete
Delete the current BioResource(s). Requires confirmation.

Rename
Rename the current BioResource.

Refresh
Refresh the current BioResource. If this is a folder, re-read the folder from persistent medium (disk).

Unload
If a BioResource is loaded and parsed into memory (denoted by a green overlay), it will be unloaded from memory.

Expand all

Collapse all

Some of the most commonly plugin-contributed actions are listed here for convenience:

Convert...
This action allows for saving of the BioResource in another format.

ApplicationRunner also contributes actions here. If you add the reference PyMol ExternalAction (see the tutorial "Run external applications from within Bioclipse") it will be accessible from here.