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

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To quickly illustrate the power of the Jmol console, open the console in the Jmol window to the right and type the following commands:

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):

<ul>

<li>select all

<li>color cpk

<li>color cpk (colours by atom type)

<li>

<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>

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.

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>.

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: all commands are only performed on the last selected atoms!

==References and Acknowledgements==

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])

Jmol: an open-source Java viewer for chemical structures in 3D. [http://www.jmol.org/ http://www.jmol.org/]

RasMol

4HHB

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.

Key reference for PDB entry 4HHB:

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.

@@ Line 111: / Line 111: @@
 <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:<br/>
+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/>
 <ul>
 <li>select all
-<li>color cpk
+<li>color cpk (colours by atom type)
-<li>
+<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>
 <br/>
-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.<br/>
+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/>
 <br/>
+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/>
+<br/>
 {{Clear}}
 ==References and Acknowledgements==
 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/>
+<br/>
 Jmol: an open-source Java viewer for chemical structures in 3D. [http://www.jmol.org/ http://www.jmol.org/] <br/>
-RasMol
+<br/>
-HHB
+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/>
+<br/>
+Key reference for PDB entry 4HHB:<br/>
+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.