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| </ol> | | </ol> |
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| ==Method II==
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| <table style="background:#ffe0e0"><tr><td>
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| <font style="font-size:140%;">Method II</font> is more complicated than Method I, and is needed only if you are using Mac '''OS X''' and wish to use '''Java'''.
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|
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| To minimize confusion: We will '''not use Java''' in Proteopedia in order to capture the desired scene. But we '''will use Java''' when we run FirstGlance to generate the animation.
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| Display the desired molecular scene in Proteopedia. JSmol without Java is fine for this step. Then:
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| <ol>
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| <li>Right click near the top of JSmol to open the JSmol menu. Click on <i>Console</i>.</li>
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| [[Image:Jsmol-menu-console.png|350 px|center]]
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|
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| <li>Enter <b>write spt "filename.txt"</b> (where "filename" is something descriptive) in the lower part of the yellow-framed Jmol_S Console box that opens. Note that "'''spt'''" is critical after "write". (The file is saved as .txt because OS X deems downloaded files with names ending in .spt to be dangerous and blocks their use.)</li>
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|
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| [[Image:Jsmol-console-write-spttxt.png|center]]
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|
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| <li>Click OK in the file save dialogs. The file will be saved in the location specified in the preferences of the browser you are using.</li>
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| <li>Open the .txt file in ''TextEdit.app'' (or another [[Help:Plain text editors|plain text editor]] such as TextWrangler or BBEdit). Block select everything (Cmd-A) and copy (Cmd-C).
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| </li>
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| [[Image:Textedit-with-blocked-spt.png|500px|center]]
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|
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| <li>Use Firefox or Safari which support Java. Chrome does not support Java.
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| </li>
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|
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| <li>Go to [http://firstglance.jmol.org FirstGlance in Jmol].
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| Check "Use Java". (Here are instructions for [[Installing and enabling Java]].)</li>
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| </li>
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|
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| <li>Display '''4QXX''' in FirstGlance. (This simple peptide avoids some problems.)
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| </li>
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|
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| <li>Verify that you are using Java. The frank at the lower right corner of Jmol should be
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| <font color="red">Jmol_S</font>, not <font color="orange">JSmol</font>.
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| </li>
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|
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| <li>Open the Jmol Console as in step #1 above.
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| </li>
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|
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| <li>Click in the lower section of the Jmol console box. Paste the text into the box. '''Cmd-V probably will not work. Use <span style="font-size:140%;">Ctrl-V.</span>''' If that doesn't work, try dragging the entire block-selected text from TextEdit and dropping it into the lower section of the Jmol Console.
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| </li>
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| [[Image:Script-into-jmol-console.png|center]]
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|
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| <li>Click the ''Run'' button at the lower left of the console box. The molecular scene from Proteopedia should appear in less than one minute.
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| <ul>
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| <li>
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| You may use the Spin, Background, Quality and Zoom buttons. Clicking other things in FirstGlance may ruin your scene, but then you can easily restore it by going back to step #10.
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| </li>
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| </ul>
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| </li>
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|
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| <li>Click on ''Save Image or Animation for Powerpoint'', and choose ''Save Animation''.</li>
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| [[Image:Fgij-arrows-12.png|500 px|center]]
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|
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| <li>Follow the instructions that appear in the lower left panel of FirstGlance to save your animation GIF file.
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| <ul>
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| <li>
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| Sometimes you may get a message "ERROR: capture canceled". In that case, quit your browser and restart it. Then go back to step #5 above and continue. We don't know why this error sometimes occurs, or how to prevent it. We have seen it only when using Java. Quitting and restarting the browser has always succeeded in our tests.
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| </li>
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| </ul>
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| </li>
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| <li>Drag the saved GIF file and drop it into a slide in your presentation.</li>
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|
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| </ol>
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|
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| </td></tr></table>
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|
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|
| ==Feedback== | | ==Feedback== |
| Problems? Unclear? Please send feedback or questions to [[Image:Contact-email.png]]. | | Problems? Unclear? Please send feedback or questions to [[Image:Contact-email.png]]. |
