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

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Click on the orange atom in the centre of the haem (iron) and the molecule should centre there - try rotating to see the effect.
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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A different type of view with bonds shown as sticks and atoms shown as smaller spheres) can be obtained using the following menu choices:<br/>
A different type of view with bonds shown as sticks and atoms shown as smaller spheres) can be obtained using the following menu choices:<br/>
&nbsp; &nbsp;'''''Main | Select | None''''' (this resets the selection to nothing) <br/>
&nbsp; &nbsp;'''''Main | Set picking | Select molecule''''' (then click on the haem group to be viewed)<br/>
&nbsp; &nbsp;'''''Main | Set picking | Select molecule''''' (then click on the haem group to be viewed)<br/>
&nbsp; &nbsp;'''''Style | Atoms | 25% van der Waals'''''<br/>
&nbsp; &nbsp;'''''Style | Atoms | 25% van der Waals'''''<br/>
&nbsp; &nbsp;'''''Style | Bonds | 0.20A'''''<br/>
&nbsp; &nbsp;'''''Style | Bonds | 0.20A'''''<br/>
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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/>
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/>
&nbsp; &nbsp;'''''Main | Select | None''''' (this resets the selection to nothing) <br/>
&nbsp; &nbsp;'''''Select | Protein | By residue name | His''''' (the number in brackets gives the occurrence of that residue type in the protein)<br/>
&nbsp; &nbsp;'''''Select | Protein | By residue name | His''''' (the number in brackets gives the occurrence of that residue type in the protein)<br/>
&nbsp; &nbsp;'''''Style | Atoms | 25% van der Waals'''''<br/>
&nbsp; &nbsp;'''''Style | Atoms | 25% van der Waals'''''<br/>
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&nbsp; &nbsp;'''''Main | Set picking | Select group''''' - then click on the haem group and the two nearby histidines.<br/>
&nbsp; &nbsp;'''''Main | Set picking | Select group''''' - then click on the haem group and the two nearby histidines.<br/>
&nbsp; &nbsp;'''''Main | Select | Display Selected Only'''''<br/>
&nbsp; &nbsp;'''''Main | Select | Display Selected Only'''''<br/>
A checkbox should appear and you will have one haem group and two histidines displayed in "ball-and-stick" mode ("Check Section")<br/>
A checkbox should appear and you will have one haem group and two histidines displayed in "ball-and-stick" mode (<scene name='User:James_D_Watson/Using_Jmol/Haemoglobin_checkpoint3/1'>"Check Section"</scene>). 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? <br/>
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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? <br/>
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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.<br/>
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.<br/>
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