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

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=== Bound ligands and solvent ===

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.

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:

In the example shown there are a number of water molecules which is confusing the identification of any ligands. To remove these atoms:

'''''Select | Hetero | All Water'''''

'''''Main | Style | Atoms | Off'''''

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'').

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:

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'''''Style | Atoms | Off'''''

'''''Main | Set picking | Center'''''

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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'''''Style | Atoms | 25% van der Waals'''''

'''''Style | Bonds | 0.20A'''''

It is known that the haem group in haemoglobin is bound tightly to a histidine residue (the proximal histidine). To identify this residue use the following set up selections:

'''''Main | Select | None''''' (this resets the selction to nothing)

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'''''Style | Atoms | 25% van der Waals'''''

'''''Style | Bonds | 0.20A'''''

The screen will now fill with all the histidines in all chains, but this is cluttered. It is evident that there are two histidines particularly close to the haem group (one above and one below). To restict the view to these two groups and the haem we will use the picking tool followed by "view selected only":

'''''Main | Select | None''''' (this resets the selction to nothing)

@@ Line 58: / Line 58: @@
 === Bound ligands and solvent ===
+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. <br/>
 <applet load='4hhb' size='400' frame='true' align='left' caption='Haemoglobin molecule - het groups' scene='User:James_D_Watson/Using_Jmol/Haemoglobin_checkpoint1/1'/>
-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/>
+In the example shown there are a number of water molecules which is confusing the identification of any ligands. To remove these atoms:<br/>
 &nbsp; &nbsp;'''''Select | Hetero | All Water'''''<br/>
 &nbsp; &nbsp;'''''Main | Style | Atoms | Off'''''<br/>
+<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/>
@@ Line 71: / Line 74: @@
 &nbsp; &nbsp;'''''Style | Atoms | Off'''''<br/>
 &nbsp; &nbsp;'''''Main | Set picking | Center'''''<br/>
+<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.
 <br/>
@@ Line 77: / Line 81: @@
 &nbsp; &nbsp;'''''Style | Atoms | 25% van der Waals'''''<br/>
 &nbsp; &nbsp;'''''Style | Bonds | 0.20A'''''<br/>
+<br/>
 It is known that the haem group in haemoglobin is bound tightly to a histidine residue (the proximal histidine). To identify this residue use the following set up selections:<br/>
 &nbsp; &nbsp;'''''Main | Select | None''''' (this resets the selction to nothing) <br/>
@@ Line 82: / Line 87: @@
 &nbsp; &nbsp;'''''Style | Atoms | 25% van der Waals'''''<br/>
 &nbsp; &nbsp;'''''Style | Bonds | 0.20A'''''<br/>
+<br/>
 The screen will now fill with all the histidines in all chains, but this is cluttered. It is evident that there are two histidines particularly close to the haem group (one above and one below). To restict the view to these two groups and the haem we will use the picking tool followed by "view selected only":<br/>
 &nbsp; &nbsp;'''''Main | Select | None''''' (this resets the selction to nothing) <br/>