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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.
==Demonstration Examples==
* [https://docs.google.com/presentation/d/1t-hAL5AWeGmXJdanNNusIbiLN0_c53laQe7PJrjQRe8/edit?usp=sharing In Google Slides]
* [http://bioinformatics.org/firstglance/fgij/ppt/animations-from-firstglance.pptx Download in Microsoft Powerpoint]


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


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).


*<font style="font-size:130%;">Mac OS X</font>:
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.
**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==
==Demonstration Examples==
Display the desired molecular scene. Then:
* [https://docs.google.com/presentation/d/1t-hAL5AWeGmXJdanNNusIbiLN0_c53laQe7PJrjQRe8/edit?usp=sharing In Google Slides]
<ol>
* [http://bioinformatics.org/firstglance/fgij/ppt/animations-from-firstglance.pptx Download in Microsoft Powerpoint]
<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 "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>
==Limitations==
 
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.
[[Image:Jsmol-console-write-spt.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>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 often 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.
If you need the faster generation of animations that Java can accomplish, use Method II.
</li>
</ul>
 
<li>Display ''any molecule'' in FirstGlance (1d66 is fine). </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>
 
<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.</li>
 
<li>Drag the saved GIF file and drop it into a slide in your presentation.</li>
 
</ol>


==Method II==
But here are [http://firstglance.jmol.org/videocapture.htm methods for capturing videos] that enable you to capture any activity on your screen, including morphs etc., and these methods are not difficult.
<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'''.


Also, 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]].


==Procedure==
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 spt "filename.txt"</b> (where "filename" is something descriptive) in the lower part of the yellow-framed JSmol Console box that opens. Note that "'''spt'''" is critical after "write". (The file is saved as .txt because OS X blocks use of files with names ending in .spt.)</li>


[[Image:Jsmol-console-write-spttxt.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>Right click [http://firstglance.jmol.org FirstGlance in Jmol] to open it in a new tab/window, so that this procedure remains available.


<li>Open the .txt file in ''TextEdit.app'' (or another plain text editor such as TextWrangler or BBEdit). Block select everything (Cmd-A) and copy (Cmd-C).
<li>Display '''4QXX''' in FirstGlance. (This simple peptide avoids some problems.)
</li>
</li>
[[Image:Textedit-with-blocked-spt.png|500px|center]]


<li>Use Firefox or Safari which support Java. Chrome does not support Java.
<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>
<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 script file in again.
</li>
</li>
 
</ul>
<li>Go to [http://firstglance.jmol.org FirstGlance in Jmol].
Check "Use Java". (Here are instructions for [[Installing and enabling Java]].)</li>
</li>
</li>


<li>Display ''any molecule'' in FirstGlance (1d66 is fine). </li>
<li>Click on ''Save Image or Animation for Powerpoint'', and choose ''Save Animation''.</li>
[[Image:Fgij-arrows-12.png|center]]


<li>Verify that you are using Java. The frank at the lower right corner of Jmol should be
<li>Follow the instructions that appear to save your animation GIF file.
<font color="red">Jmol_S</font>, not <font color="orange">JSmol</font>.
</li>
</li>
<li>Open the Jmol Console as in step #1 above.
</li>
<li>Click in the lower section of the yellow-framed console box. Paste the text into the box. '''Cmd-V probably will not work. Use Ctrl-V.'''
</li>
<li>Click the ''Run'' button at the lower left of the yellow-framed console box. The molecular scene from Proteopedia should appear in less than one minute.</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.</li>


<li>Drag the saved GIF file and drop it into a slide in your presentation.</li>
<li>Drag the saved GIF file and drop it into a slide in your presentation.</li>
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</ol>
</ol>


</td></tr></table>
==Animation Kit==
To enable you to make animations with full control, 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 18:27, 14 March 2026

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 Examples

Limitations

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.

But here are methods for capturing videos that enable you to capture any activity on your screen, including morphs etc., and these methods are not difficult.

Also, 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 .

Procedure

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 Kit

To enable you to make animations with full control, FirstGlance provides a downloadable Animation Kit with complete instructions.

Feedback

Problems? Unclear? Please send feedback or questions to .

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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