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

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   '''''Main | Console | Open'''''  
   '''''Main | Console | Open'''''  
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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  
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 go to the Jmol homepage and look up the documentation at [http://jmol.sourceforge.net/ http://jmol.sourceforge.net/].<br/>
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<applet load='4hhb' size='400' frame='true' align='right' caption='Haemoglobin molecule' scene='User:James_D_Watson/Using_Jmol/Haemoglobin_start2/1'/>


To quickly illustrate the power of the Jmol console, open the console in the Jmol window to the right and type the following commands (use "Ctrl+Enter" after each command to start a new line for the next command in the series):<br/>
Type the following command:  
<ul>
select all
<li>select all
and click the "Execute" button on the Console. Jmol writes a few things into the upper part of the Console window after executing the command, including the number of atoms selected.
<li>color cpk (colours by atom type)
<li>restrict *b (restricts the selection to chain b)
<li>centre selected
<li>select [HEM]&*b (select all HEM groups from chain b)
<li>spacefill 50% (display selected residues as 50% spacefill)
<li>color purple
<li>center selected
<li>select HIS &*b (select all Histidine residues from chain b)
<li>color green
<li>spacefill 50%
<li>restrict HEM,his63,his92
</ul>
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Once entered, click on the "Execute" button on the Console - you will see a number of things being written into the upper part of the Console window followed by the display changing. You can also press enter or click on "Execute" at any stage to see the effect each command has.<scene name='User:James_D_Watson/Using_Jmol/Haemoglobin_final_script/1'>"Click here to see the end result"</scene>.<br/>
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You can see how if you build up a series of useful scripts you can rapidly display different proteins in the same way (or highlight the same aspects). It should also be noted that you can select a list of commands from a text editor and copy-paste them into the Console command area as a single script to be run. Please feel free to play with different commands - but remember: <b>all commands are only performed on the last selected atoms!</b><br/>
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Now type:
{{Clear}}
color purple
==References and Acknowledgements==
and click the "Execute" button again.
This tutorial was inspired by the "Interactive Concepts In Biochemistry" Structure Tutorials published by John Wiley & Sons ([http://www3.interscience.wiley.com:8100/legacy/college/boyer/0471661791/structure/structure.htm http://www3.interscience.wiley.com:8100/legacy/college/boyer/0471661791/structure/structure.htm])<br/>
 
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And finally, type:
Jmol: an open-source Java viewer for chemical structures in 3D. [http://www.jmol.org/ http://www.jmol.org/] <br/>
spacefill 100%
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and click "Execute".
RasMol: Biomolecular graphics for all [http://www.openrasmol.org/ http://www.openrasmol.org/]. Original reference: Roger A. Sayle and E. James Milner-White, Trends in Biochemical Sciences 20(Sept):374-376, 1995. <br/>
 
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Key reference for PDB entry 4HHB:<br/>
The Console allows very powerful control of Jmol with the command language. You can see a listing of Jmol commands at the Jmol interactive scripting documentation page (opens a new window).  
G.Fermi et al. (1984). The crystal structure of human deoxyhaemoglobin at 1.74 A resolution. J Mol Biol, 175, 159-174. PubMed id: 6726807.
 
Now that you are more familiar with Jmol, click below to move to the section on protein secondary structure.
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