User:James D Watson/Using Jmol: Difference between revisions

Displaying the entire protein as spacefill spheres gives a better impression of the actual shape of the protein. In this case the four subunits are clearly packed together with little space between them. It is also evident that there are a number of small molecules bound to the protein surface. These are often solvent molecules (water, deuterium, etc) or artefacts of the crystallisation process (glycerol, etc), but they can also represent substrate mimics, inhibitors and cofactors. In the example shown there are a number of water molecules which is confusing the identification of any ligands. To remove these atoms:<br/>

This leaves the remaining bound small molecules (<scene name='User:James_D_Watson/Using_Jmol/Haemoglobin_checkpoint2/1'>"Check Section"</scene>). Explore the structure some more to confirm the identity of these tightly bound molecules as the haem groups (''Hint: Toggle off the spinning and click on the Jmol window. Moving your cursor over an atom should provide a pop-up window identifying that atom/residue'').<br/>

Now let's focus in on a haem group to see how it interacts with the protein. To restrict the view to just the ligand molecules perform the following menu choices:<br/>

Click on the orange atom in the centre of the haem (iron) and the molecule should centre there - try rotating to see the effect.

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