Help:Making animations for Powerpoint

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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.

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).

Contents

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. 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 Image:Contact-email.png.

Choose A Method

  • Windows: Use Method I.


  • Mac OS X:
    • 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 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:

  1. Right click near the top of JSmol to open the JSmol menu. Click on Console.
  2. Enter write "filename.spt" (where "filename" is something descriptive) in the lower part of the yellow-framed JSmol Console box that opens. Be sure to include .spt as the last 4 characters of the filename.
  3. 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.
  4. Go to FirstGlance in Jmol.
    • 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, 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.
    • 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.
  5. Display 4QXX in FirstGlance. (This simple peptide avoids some problems.)
  6. 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.
    • 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.
  7. Click on Save Image or Animation for Powerpoint, and choose Save Animation.
  8. Follow the instructions that appear in the lower left panel of FirstGlance to save your animation GIF file.
    • 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.
  9. Drag the saved GIF file and drop it into a slide in your presentation.

Method II

Method II 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:

  1. Right click near the top of JSmol to open the JSmol menu. Click on Console.
  2. Enter write spt "filename.txt" (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.)
  3. 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.
  4. 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).
  5. Use Firefox or Safari which support Java. Chrome does not support Java.
  6. Go to FirstGlance in Jmol. Check "Use Java". (Here are instructions for Installing and enabling Java.)
  7. Display 4QXX in FirstGlance. (This simple peptide avoids some problems.)
  8. Verify that you are using Java. The frank at the lower right corner of Jmol should be Jmol_S, not JSmol.
  9. Open the Jmol Console as in step #1 above.
  10. Click in the lower section of the Jmol console box. Paste the text into the box. Cmd-V probably will not work. Use Ctrl-V. 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.
  11. Click the Run button at the lower left of the console box. 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 going back to step #10.
  12. Click on Save Image or Animation for Powerpoint, and choose Save Animation.
  13. Follow the instructions that appear in the lower left panel of FirstGlance to save your animation GIF file.
    • 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.
  14. Drag the saved GIF file and drop it into a slide in your presentation.

Feedback

Problems? Unclear? Please send feedback or questions to Image:Contact-email.png.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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