Just load a dataset (if you wish to load a PDB fitted into a Situs file, start with the PDB) by "File" and "Open". After that there should appear an additional entry in the main gui window, with a symbol and the filename. If you loaded a PDB file, there should appear also a graphical visualization (in a simple line drawing mode).
In the picture above you can see the main gui window with two files loaded. The first file is a PDB file and the second one is a Situs file.
To adjust the visualization of a file, just select the file in the list and click on the "Properties" button (alternatively you can just double-click on the file). Now there should appear a properties dialog. This dialog is completely different for the two file types. Lets start with the properties dialog for the pdb files.
In the PDB properties dialog you can adjust the drawing modes for the molecules displayed in the main graphics window. If you click on the "Graphics" tab you should be able to see the following dialog:
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| PDB Properties - Graphics |
The drawing mode can not only affect all atoms in a PDB file, but also just some parts. With the first combo-box widget labeled with "Atoms" you can select the part you want to modify. You can adjust the drawing mode of "All" atoms, of all atoms of a certain "Type", of all atoms of a certain "Residue Name" and of just one atom with a special "Index". After that you can select the new "Graphics Mode" and the new "Color Mapping" for the selected atoms.
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| Point | Line | CPK | VDW | Dotted | Licorize |
Below the widgets concerning the drawing modes there is a so called "Graphics Mode Stack". The idea behind this is, that you can mix the drawing modes. E.g. if you want to point out some special features in the PDB file, you most probably want to draw them in a differnt way than the rest of the atoms. In this case you can first select "All" atoms and adjust their drawing mode (e.g. line mode). After that you should be able to see a single line in the stack, saying "All - Line - Color:Type". Now press the "Add" button on the bottom of the dialog. Now there should be another line saying the same "All - Line - Color:Type". You have now a second drawing mode you can adjust. Please select now the new, second line in the stack.
Now you should select a subset of the atoms, e.g. only the atoms of a special type (lets say only CA atoms), and adjust the drawing mode (e.g. set the graphics mode to "VDW"). After all this you should be able to see something like this:
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| Line and VDW Mode |
With this mixing of the drawing modes you can very easily adjust the visualization of the PDB files and get very concise results.
The Situs files are volume datasets. SenSitus provides different visualisation methods to draw these.
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| Situs Properties - Surface |
The first visualization method is a surface based representation of the volume. Click on the "Surface" tab of the dialog and type in a threshold value in the "Level" text entry widget. The program will now connect all points in your Situs density map where the value reaches this level value. Now click on "Create Isosurface".
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| Surface |
You can make the surface transparent by dragging the "Transparency" slider to the left. By enabling the "Fast Transparency Mode", the program will use a "faked" method, which can be much faster (depends on the opengl implementation and hardware).
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| Transparent Surface |