Conformational Search Browser Help

Figure 2: The Display Tab. This tab contains the controls for the viewer display (the java applet), atom rendering for all molecules and the conformation browser.

The Display Tab

Tab Menu

1: Tab Selection menu. The colour of the selected tab is cyan while other tabs are blue.

Browse Conformations

2: Browse trough the conformations by the +1 or –1 button. The number of the selected conformation is displayed. You can key in a number (don’t hit enter afterwards as the page will reload) and browse on from that.

Atom Display Controls

3: The pull-down menu sets the atom display style (rendering) for the active molecule.

4: The pull-down menu sets the atom colouring scheme for the active molecule.

Surface

5: The buttons display the surface of the selected molecule on/off.

6: The pull-down menu selects the colour of the active surface.

7: The pull-down menu sets the transparency of the active surface.

8: The pull-down menu sets the texture of the active surface. Works only with amino acids, i.e. the molecule must be a peptide.

9: The buttons display the mesh surface of the selected molecule on/off.

10: The pull-down menu selects the colour of the active mesh surface.

Molecule Display Controls

11: The pull-down menu sets the atom display style (rendering) for all molecules.

12: The pull-down menu sets the atom colouring scheme of all molecules.

13: The buttons display all molecules on/off.

Viewer Display Controls

14: The checkbox turns Shadows on/off.

15: The checkbox turns Antialiasing on/off.

16: The pull-down menu sets the background colour.

17: The pull-down menu will set a gradient on the background colour. You can choose the top colour, but the bottom colour is black.

Figure 3: The Help Tab. This tab contains help on mouse and keyboard controls as well as links to help files and the conformational search log files.

The Help Tab

Tab Menu

1: Tab Selection menu. The colour of the selected tab is cyan while other tabs are blue.

Key Action Menu

2: Help on mouse and keyboard controls.

Links & Logfiles Menu

3: Link to Pharmacophore Browser Help.

4: Link to Astex Viewer Help.

5: Link to MacroModel Log file. This is the log-file from the conformational search containing the conformational energies in the summary at the end.

6: Link to Ligprep Log file. This is the log-file from the 3D conversion of the 2D input structure.

7: Download SD-file. Link to an SD-file containing all the conformations/molecules/pharmacophore model.

8: Link to this page. Opens the page without frames (in full view). Copy this link and insert it in Powerpoint etc. for presentations.