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

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</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. You can also press enter or click on "Execute" at any stage to see the effect each command has.

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!

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==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/]

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 </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. You can also press enter or click on "Execute" at any stage to see the effect each command has.<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/>
@@ Line 135: / Line 135: @@
 ==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/>
 <br/>