Pharmacophore Browser Help

Figure 1: The Molecule Tab (Number of Molecule Tabs may vary). This tab contains the controls for the each of the molecules. You can on/off the display for each molecule as well as its surface.

The Molecule Tab. (Number of tabs may vary)

Tab Menu

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

Conformation – Surface

2: The checkbox turns atom display of the molecule on/off.

3: The pull-down menu selects the atom display style (rendering) of the molecule.

4: The pull-down menu selects the colouring scheme of the molecule.

5: The checkbox turns surface display of the molecule on/off.

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

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

Figure 2: The Browse Tab. This tab contains the molecule browser and atom rendering for all molecules.

The Browse 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.

Figure 3: The Display & Help Tab. This tab contains the controls for the viewer display (the java applet), help on keyboard and mouse controls as well as links to help pages.

The Display & Help Tab

Tab Menu

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

Viewer Display Controls

2: The checkbox turns Shadows on/off.

3: The checkbox turns Antialiasing on/off.

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

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

Key Action Menu

6: Help on mouse and keyboard controls.

Links & Logfiles Menu

7: Link to Pharmacophore Browser Help.

8: Link to Astex Viewer Help.

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

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