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

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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 HERE"<br/>
A checkbox should appear and you will have one haem group and two histidines displayed in "ball-and-stick" mode ("Check Section")<br/>
<br/>
<br/>
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/>
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/>
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/>
<br/>
<br/>
{{Clear}}
{{Clear}}


The Jmol Console
==The Jmol Console==
Jmol can also be controlled using a command language. Knowing even a few simple commands can useful. To access the Console, use the Jmol menu:
Jmol can also be controlled using a command language based on the commands from RasMol. This is effectively a scripting system and the use of a handful of simple commands can replace the use of a greater number of menu choices. To access the Console, use the Jmol menu:
 
<br/>
Console... | Open
&nbsp; &nbsp;'''''Main | Console | Open'''''
 
<br/>
A small window, the Jmol Console, will appear at the upper left corner of your screen. A cursor will be blinking in the lower part of the window. This is where you can enter commands.
A small popup window will appear. This is the Jmol Console, in which a cursor will be blinking - this is where you can enter commands. For a full list of commands please


   
   
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