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Any molecular scene in Proteopedia (or any Jmol website) can be converted to a rocking or spinning animation for presentations, such as Microsoft Powerpoint, free Google Slides, or free Libre Office.
Any molecular scene in Proteopedia (or any Jmol website) can be converted to a rocking or spinning animation for presentations, such as Microsoft Powerpoint, free Google Slides, or free Libre Office.


Making presentation-ready animations is a feature of [[FirstGlance in Jmol]] version 2.5, installed into Proteopedia in early June, 2016. If you want to animate a molecular scene that you obtain in FirstGlance in Jmol, then you don't need the methods below. The capability is built into FirstGlance: see the snapshot in step #7 below (in Method I).
Proteopedia has a built-in mechanism to make a presentation-ready animation. Simply click on ''Export Animated Image'' below the molecular scene. You can also export a static image there.
 
In February, 2019, Proteopedia's mechanism is somewhat limited. The animations are jerky and will perhaps be smaller than you wish. An alternative is to make an animation of a Proteopedia scene using [[FirstGlance in Jmol]].
 
Making presentation-ready animations in ''FirstGlance in Jmol'' is quick and easy, and the animations will rotate more smoothly and can be larger (hence clearer/sharper).
 
If you want to animate a molecular scene that you first obtain in FirstGlance in Jmol, then you don't need the methods below. The capability is built into FirstGlance: see the snapshot in step #7 below (in Method I). The methods below are only for generating an animation in FirstGlance from a scene in Proteopedia.


==Demonstration Examples==
==Demonstration Examples==
Line 10: Line 16:
This method will make a presentation-ready rocking or spinning animation of a fixed molecular scene. See examples linked above. It will not convert complex Jmol animations such as [[Morphs]] or those in [[Molecular Playground/HIV Protease Inhibitor]] and [[Molecular Playground/Tamiflu]] into presentation-ready animations. However, morphs can be made presentation-ready using [http://polyview.cchmc.org/polyview3d.html Polyview-3D]. An example is the last slide in this downloadable [http://bioinformatics.org/firstglance/fgij/ppt/polyview-3d-examples.ppt Powerpoint demonstration of Polyview-3D animations]. If you need help with a morph, please email [[Image:Contact-email.png]].
This method will make a presentation-ready rocking or spinning animation of a fixed molecular scene. See examples linked above. It will not convert complex Jmol animations such as [[Morphs]] or those in [[Molecular Playground/HIV Protease Inhibitor]] and [[Molecular Playground/Tamiflu]] into presentation-ready animations. However, morphs can be made presentation-ready using [http://polyview.cchmc.org/polyview3d.html Polyview-3D]. An example is the last slide in this downloadable [http://bioinformatics.org/firstglance/fgij/ppt/polyview-3d-examples.ppt Powerpoint demonstration of Polyview-3D animations]. If you need help with a morph, please email [[Image:Contact-email.png]].


==Choose A Method==
*<font style="font-size:130%;">Windows:</font> Use Method I.




*<font style="font-size:130%;">Mac OS X</font>:
==Procedure==
**If you only have one or a few animations to make, use '''Method I without Java'''. Method I is easiest, but you will have to wait several minutes for each animation to be generated in FirstGlance in Jmol.
**If you are making many animations, or animating larger models (>5,000 atoms) in high quality, you may prefer to use '''[[#Method II|Method II]] with Java'''. Method II is fussier to do and requires Java, but the animations will be generated by FirstGlance in Jmol in less than one-tenth the time required by Method I.
 
==Method I==
Display the desired molecular scene. Then:
Display the desired molecular scene. Then:
<ol>
<ol>
<li>Right click near the top of JSmol to open the JSmol menu. Click on <i>Console</i>.</li>
<li>Right click (Macs: Ctrl-click) near the top of JSmol to open the JSmol menu. Touch <i>File</i>, then <i>Save</i>, then click on '''Save script with state'''.</li>
[[Image:Jsmol-menu-console.png|350 px|center]]
[[Image:Jsmol-menu-save-script-with-state.png|center]]


<li>Enter <b>write "filename.spt"</b> (where "filename" is something descriptive) in the lower part of the yellow-framed JSmol Console box that opens. Be sure to include <span style="font-size:150%;">'''.spt'''</span> as the last 4 characters of the filename.</li>


[[Image:Jsmol-console-write-spt.png|center]]
<li>Change the file name if you wish. The conventional file type is '''.spt''' but the file name does not matter. Complete the file saving dialogs. The file will be saved in the location specified in the preferences of the browser you are using.</li>
 
<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>
 
<li>Go to [http://firstglance.jmol.org FirstGlance in Jmol].
<ul>
<li>'''Windows:'''
Check "Use Java" if you have Java installed. Using Java will generate animations more than ten times faster. (Here are instructions for [[Installing and enabling Java]].) If you are using Java, [http://bioinformatics.org/firstglance/fgij/slides.htm#browsers '''Firefox''' is recommended]. We do ''not recommend Internet Explorer'' because it sometimes (especially in Windows 7) saves a defective (empty, zero bytes) animation GIF file with Java, and is impossibly slow without Java. Chrome and Edge do not support Java, but are OK if you are not using Java.</li>


<li>'''Mac OS X: Do not use Java.''' You cannot drop the spt file into the Jmol_S Java applet in OS X.
<li>Right click [http://firstglance.jmol.org FirstGlance in Jmol] to open it in a new tab/window, so that this procedure remains available.
If you need the faster generation of animations that Java can accomplish, use Method II.
</li>
</ul>


<li>Display '''4QXX''' in FirstGlance. (This simple peptide avoids some problems.)
<li>Display '''4QXX''' in FirstGlance. (This simple peptide avoids some problems.)
</li>
</li>


<li>Drag the SPT file and drop it into JSmol/Jmol_S in FirstGlance. The molecular scene from Proteopedia should appear in less than one minute.
<li>Drag the &quot;script with state&quot; file that you saved above and drop it into JSmol (drop on top of the molecule) in FirstGlance. The molecular scene from Proteopedia should appear in less than one minute.
<ul>
<ul>
<li>
<li>
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 dropping the SPT file in again.
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 dropping the script file in again.
</li>
</li>
</ul>
</ul>
Line 52: Line 41:


<li>Click on ''Save Image or Animation for Powerpoint'', and choose ''Save Animation''.</li>
<li>Click on ''Save Image or Animation for Powerpoint'', and choose ''Save Animation''.</li>
[[Image:Fgij-arrows-12.png|500 px|center]]
[[Image:Fgij-arrows-12.png|center]]


<li>Follow the instructions that appear in the lower left panel of FirstGlance to save your animation GIF file.
<li>Follow the instructions that appear to save your animation GIF file.
<ul>
<li>
If you are using Java in Windows, occasionally you may get a message "ERROR: capture canceled". In that case, quit your browser and restart it. Then go back to step #4 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.
</li>
</ul>
</li>
 
<li>Drag the saved GIF file and drop it into a slide in your presentation.</li>
 
</ol>
 
==Method II==
<table style="background:#ffe0e0"><tr><td>
<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'''.
 
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.
 
 
Display the desired molecular scene in Proteopedia. JSmol without Java is fine for this step. Then:
<ol>
<li>Right click near the top of JSmol to open the JSmol menu. Click on <i>Console</i>.</li>
[[Image:Jsmol-menu-console.png|350 px|center]]
 
<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>
 
[[Image:Jsmol-console-write-spttxt.png|center]]
 
<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>
 
<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).
</li>
[[Image:Textedit-with-blocked-spt.png|500px|center]]
 
<li>Use Firefox or Safari which support Java. Chrome does not support Java.
</li>
 
<li>Go to [http://firstglance.jmol.org FirstGlance in Jmol].
Check "Use Java". (Here are instructions for [[Installing and enabling Java]].)</li>
</li>
 
<li>Display '''4QXX''' in FirstGlance. (This simple peptide avoids some problems.)
</li>
 
<li>Verify that you are using Java. The frank at the lower right corner of Jmol should be
<font color="red">Jmol_S</font>, not <font color="orange">JSmol</font>.
</li>
 
<li>Open the Jmol Console as in step #1 above.
</li>
 
<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.
</li>
[[Image:Script-into-jmol-console.png|center]]
 
<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.
<ul>
<li>
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.
</li>
</ul>
</li>
 
<li>Click on ''Save Image or Animation for Powerpoint'', and choose ''Save Animation''.</li>
[[Image:Fgij-arrows-12.png|500 px|center]]
 
<li>Follow the instructions that appear in the lower left panel of FirstGlance to save your animation GIF file.
<ul>
<li>
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.
</li>
</ul>
</li>
</li>


Line 132: Line 50:
</ol>
</ol>


</td></tr></table>
==Animation Kit==
FirstGlance in Jmol's built-in animation maker also has limitations on the size of the animation, particularly if you want 360° spinning. To enable you to make such animations as large and crisp as you like, FirstGlance provides a [https://bioinformatics.org/firstglance/fgij/animation_kit_instructions.pdf downloadable Animation Kit] with complete [https://bioinformatics.org/firstglance/fgij/animation_kit_instructions.pdf instructions].


==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]].

Latest revision as of 21:23, 9 August 2020

Any molecular scene in Proteopedia (or any Jmol website) can be converted to a rocking or spinning animation for presentations, such as Microsoft Powerpoint, free Google Slides, or free Libre Office.

Proteopedia has a built-in mechanism to make a presentation-ready animation. Simply click on Export Animated Image below the molecular scene. You can also export a static image there.

In February, 2019, Proteopedia's mechanism is somewhat limited. The animations are jerky and will perhaps be smaller than you wish. An alternative is to make an animation of a Proteopedia scene using FirstGlance in Jmol.

Making presentation-ready animations in FirstGlance in Jmol is quick and easy, and the animations will rotate more smoothly and can be larger (hence clearer/sharper).

If you want to animate a molecular scene that you first obtain in FirstGlance in Jmol, then you don't need the methods below. The capability is built into FirstGlance: see the snapshot in step #7 below (in Method I). The methods below are only for generating an animation in FirstGlance from a scene in Proteopedia.

Demonstration ExamplesDemonstration Examples

LimitationsLimitations

This method will make a presentation-ready rocking or spinning animation of a fixed molecular scene. See examples linked above. It will not convert complex Jmol animations such as Morphs or those in Molecular Playground/HIV Protease Inhibitor and Molecular Playground/Tamiflu into presentation-ready animations. However, morphs can be made presentation-ready using Polyview-3D. An example is the last slide in this downloadable Powerpoint demonstration of Polyview-3D animations. If you need help with a morph, please email .


ProcedureProcedure

Display the desired molecular scene. Then:

  1. Right click (Macs: Ctrl-click) near the top of JSmol to open the JSmol menu. Touch File, then Save, then click on Save script with state.


  2. Change the file name if you wish. The conventional file type is .spt but the file name does not matter. Complete the file saving dialogs. The file will be saved in the location specified in the preferences of the browser you are using.
  3. Right click FirstGlance in Jmol to open it in a new tab/window, so that this procedure remains available.
  4. Display 4QXX in FirstGlance. (This simple peptide avoids some problems.)
  5. Drag the "script with state" file that you saved above and drop it into JSmol (drop on top of the molecule) in FirstGlance. The molecular scene from Proteopedia should appear in less than one minute.
    • 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 dropping the script file in again.
  6. Click on Save Image or Animation for Powerpoint, and choose Save Animation.
  7. Follow the instructions that appear to save your animation GIF file.
  8. Drag the saved GIF file and drop it into a slide in your presentation.

Animation KitAnimation Kit

FirstGlance in Jmol's built-in animation maker also has limitations on the size of the animation, particularly if you want 360° spinning. To enable you to make such animations as large and crisp as you like, FirstGlance provides a downloadable Animation Kit with complete instructions.

FeedbackFeedback

Problems? Unclear? Please send feedback or questions to .

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz
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