Getting Started with Bioclipse

Prerequisites

Installation

See the tutorial: Installing Bioclipse.

First startup

Upon first startup you are asked to set a new root folder.

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Select a folder where you have molecules, or where you would like to have your base folder for moelcules. In this tutorial we will install sample data provided with the bioclipse installation, so simply select any place on your harddisk (such as your home folder).

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Some explanations


Installing sample data

1) Place yourself in the BioResource Navigator where you'd like to create the directory with sample data.
2) In the menu, select "Operations -> install sample data"
3) Confirm, and a directory will be installed entitled "Sample data" containeng various resources for testing

View/Edit molecules

Double-click a molecule in the BioResourceView. See the 2D-editor open if the molecule contains 2D-coordinates, and see the 3D-view (Jmol) open if the molecule contains 3D-coordinates. Try some editing in 2D and try rotating the molecule in Jmol by clicking and dragging the mouse within the Jmol View. Note that properties change depending on the file type, e.g. are PDB properties different from MOL properties.

See molecular hierarchy

Open the ChemTree by selecting in the menu: "Window -> Show View -> Other..."

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Now you can double-click on a molecule in the BioResource Navigator and see the substructure (bonds/atoms) in the ChemTree. Clicking on e.g. an atom also displays atom properties in the Properties view.

If you dooubleclick a 2D-structure that opens in JchemPaint (JCP), you can click on atoms/bonds in the ChemTree and see them highlighted in the 2D-views.

If the 3D-viewer (Jmol View) is not open, select menu alternative "Windows -> Show View -> Jmol Viewer".


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