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

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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/>
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/>
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Now let's focus in on a haem group to see how it interacts with the protein. redisplay the pigment, this time as a "ball and stick" model, and also with the atoms colored by element.
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:


Select | Hetero | Ligand
'''''Select | Protein | All'''''
Render | Scheme | Ball and Stick
'''''Style | Atoms | Off'''''
Color | Atoms | Scheme | Element (CPK)


'''''Main | Set picking | Select molecule'''''
Zoom in using the mouse to get a better look at the atoms of the pigments.
Then click on the two PO4 groups and any three of the haem groups
'''''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.


Showing specific amino acids:
A different type of view with bonds shown as sticks and atoms shown as smaller spheres) can be obtained using the following menu choices:
'''''Main | Set picking | Select molecule''''' (then click on the haem group to be viewed)
'''''Style | Atoms | 25% van der Waals'''''
'''''Style | Bonds | 0.20A'''''


Sometimes, you may want to look at a certain amino acid or a type of amino acid in a molecule. For example, some proteins are stabilized by disulfide bonds, which are covalent bonds formed between two cysteine side chains. Three disulfide briges are present in the protein insulin. First, we'll look at the overall structure of insulin.
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)
As you see, insulin is quite a small protein. To the see disulfide bonds, use the Jmol menu in the sequence below:
'''''Select | Protein | By residue name | His''''' (the number in brackets gives the occurrence of that residue type in the protein)
'''''Style | Atoms | 25% van der Waals'''''
'''''Style | Bonds | 0.20A'''''


Select | Protein | All
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":
Render | Atoms | Off
(Don't worry, it's supposed to disappear!)  
Render | Structures | Cartoon
Select | Protein | By Residue Name | CYS
Render | Bonds | 0.3 Å
Color | Disulfide Bonds | Yellow


Note that that the cartoon and stick renderings would have been hidden by the spacefilled atoms if you had neglected to turn them off. This is because the current rendering choice is not automatically turned off when another choice is selected; each rendering style is controlled individually, so multiple display styles of the same atoms are possible.
'''''Main | Select | None''''' (this resets the selction to nothing)
'''''Main | Set picking | Select group'''''
Then click on the haem group and the two nearby histidines.
'''''Main | Select | Display Selected Only'''''


A checkbox should appear and you will have one haem group and two histidines displayed in "ball-and-stick" mode. "Check HERE"
You can also change the display of disulfide bonds under Render | Disulfide Bonds, but note that they must be part of the currently selected set of atoms to be affected by the change.


Inverting selection
Rotate and look at the view. The histidine closest to the haem group is the proximal histidine and the other is the distal. What do you notice about the plane of the haem ring? Why is this relevant to the structure of deoxyhaemoglobin?


What if you want to change the display of everything except the cystines?
This concludes a basic introduction to manipulating structures in Jmol to identify interesting features using the menu choices. This exercise is by no means exhaustive, so please feel free to explore the menus and see the effects they have.


Select | Protein | By Residue Name | CYS
Select | Invert Selection
Color | Cartoon | Orange




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The Jmol Console
The Jmol Console
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