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CCP4i: Graphical User Interface |
| Graphics and Viewing Utilities |
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The layout of each task window, i.e. the number of folders present, and whether these folders are open or closed by default, depends on the choices made in the Protocol folder of the task (see Introduction). Although certain folders are closed by default, there are specific reasons why you should or may want to look at them. These reasons are described in the Task Window Layout sections below.
3D viewer for the display of proteins, ligands and electron density maps.
The output from the AstexViewer task is displayed in a browser which requires Java. Make sure CCP4i uses a suitable one, through the System Administration > Configure Interface option from the menu on the right-hand side of the Main Window. For some browsers it appears necessary to start a browser session before starting CCP4i.
Features to look out for in the AstexViewer Task Window are:
| Folder title | Importance | Comment |
|---|---|---|
| Display Options | Applet height and width | Height and width should both be given to have an effect on the applet size when displayed in a webpage. |
See program documentation: AstexViewer, AstexViewer manual.
Display tables and graphs from CCP4 formatted log files (.log) or your own free format files with simple columns of data (.dat). Be sure to use the desired File Type (and corresponding filename filter) when selecting a file for display.
See program documentation: Loggraph.
Interactive map section viewer for CCP4 formatted map files.
Contour levels can be adapted through Section > Contour Levels at the top of the MapSlicer window.
See program documentation: MapSlicer.
Molecular Visualisation Program (display atomic coordinates). Whenever user input is required (e.g. when opening a file), this should be entered at the prompt as it appears in the window where CCP4i was started. More than one PDB file can be opened and viewed at any one time, and they can be closed through File > Close, in reverse order. Exit exits the RasMol program.
See program documentation: RASMOL, RasMol Manual.
Sketchpad for drawing protein topology cartoons.
The documentation needed to get started with the program, is in the drawing canvas when the program starts up. It disappears when the cursor is brought into the drawing canvas, but can be re-called at any time by clicking the HELP! button.
See program documentation: TopDraw.
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