Animation Kit for FirstGlance in Jmol Version 4.3.
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Try the Animation Maker built into FirstGlance first.
FirstGlance can make a presentation-ready animation of any molecular view with just a few
mouse clicks. Here is how to do that. Here are examples of such animations in Google Slides.
These easily-made animations simply rock or spin. To capture more complex movements, see
the Video Capture Instructions.
This Kit is provided in case the animation-maker built into FirstGlance does not do what youwant. Sometimes the built-in mechanism fails to work. Also, if you want a full 360º spin (ratherthan rocking), the built-in mechanism is limited to a rather small size, which may get blurrywhen you put it in a slide and enlarge it. This Kit can make larger, sharper animations.
If FirstGlance's built-in animation maker gave you an error message, try it again. But before you
try it again, make a slight change by rotating the molecule a tiny bit, or resizing the browser
window a tiny bit. The built-in animation maker has two bugs. (1) If you submit exactly thesame job a second time, it fails with an error message. So, make a slight change each time youtry again. (2) if multiple people submit jobs at the same time, it crashes. So, if you make a slightchange and then try a few minutes later, it may well work.
If FirstGlance's built-in animation maker doesn't give you what you need, follow the instructions
below.

Animation Kit Instructions
1. Download the Animation Kit and unzip it. (If you downloaded it a while ago, best todownload it again in case it has been updated.) This will produce a folder (directory) named
animation_kit. The animations you create will be made in this folder.
2. Install or update Java. You will need to run the stand-alone Jmol application (included in thekit), which requires Java. Go to java.com and follow instructions to download and install thecurrent version. (Optionally, if you already have Java installed, you can verify the installedversion – see instructions under Options below.)
If you don't know where in FirstGlance to find somethingmentioned below, look it up in the How & Where Index.
3. In FirstGlance, get exactly the molecular view that you want to animate. Things to consider:
A. Usually you will want to depress the quality button. It is near the top of the Molecule
Information Tab, and in the Button Box in the Views or Tools tab.

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B. Give some thought to whether you prefer a white or black background, and set thebackground accordingly using the Background button (near the top of the Molecule
Information Tab, and in the Button Box in the Views or Tools tab).
C. Size your browser window so that JSmol is the size you want for your animation. You
can change the size later, but its simpler to start with the size and shape that you want.
The animation can be rectangular if your molecule fits better in a rectangle. Large sizes
will generate larger animation files. To avoid an unnecessarily large presentation file(.pptx), don't make the size larger than needed for a clear animation when projected. A
square 500 pixels on a side is usually large enough.
D. Zoom your molecule to fill JSmol. If there is a lot of empty space around the molecule,that empty space will be in your animation, taking up wasted space in your slide.
4. Save a png file containing the JSmol state:
A. Right click on or near the molecule in JSmol, and on the menu that appears, click on File,
Save, Save as PNG/JMOL. Be sure to save it into your animation kit folder.

B. Rename the .png file to something descriptive of the molecular view it contains (keepingthe file type/suffix .png).
5. Run Jmol: double click on the file Jmol.jar in your animation kit folder. A black window shouldappear.
macOS: The first time you run Jmol.jar, right click (control-click) on it, and select Open
With, Jar Launcher. Confirm that you wish to open it. After doing this once, you cansimply double-click Jmol.jar and it will open.
6. Display your molecular view in Jmol: The png file you saved in step 4 is special: it contains
JSmol commands to re-create your molecular view. Drag the special png file and drop it into theblack Jmol window. OK changing the window width and height to the size when you saved yourmolecular view. Your molecular view should appear.
If the slab button is depressed in your molecular view, and for Density Maps, see
Animating a Slabbed View (under Options below) for special instructions that supersede
steps 7 and 8 below.
7. Set the animation speed: Drag the file playback-slow.spt and drop it onto your molecularview. (Later, if you repeat this step, you may choose a different speed.)28. Create the animation file:
For an animation of a slab of your molecule, go to Animating a Slabbed View (under Options
farther below) – don't continue with A, B, C here. For an animation without cutting throughyour molecule, continue with A, B, C here.
A. Decide whether you want rocking or spinning. If rocking through 40, 60, or 90 degrees issufficient, the animation file will be smaller. If you need to show all sides of themolecule, you can spin (360o), but the animation file will be larger.
B. Decide whether to rock or spin around the X (horizontal) or Y (vertical) axis.
C. Drag the appropriate file and drop it onto the molecule. For example, if you want torock 60 degrees around the Y axis, drag and drop the file rock-y-60.spt. The molecule
will begin to move. Wait until it stops moving. This may take several minutes.
9. Rename the animation file: The previous step will create a file whose name begins rock orspin, and ends in .gif, in your animation_kit folder. Rename it to something appropriate(keeping .gif as the end of the file name!), because if you make another animation, it will
overwrite this file.
10. Drag the .gif file and drop it into a slide in your presentation. Resize and position as desired.
In Google Slides or recent versions of PowerPoint, it will animate automatically. In older
versions of PowerPoint, it will animate only when you go into Slideshow/Projection mode.
(Optional: you can preview the animation by dragging the .gif file and dropping it into a web
browser window.)
Repeat steps 3-10 to make additional animations.
If you have any problems with the animation kit, we'd like to help, and to know how to improve
it. Please contactOptions
Adjusting animation size, zoom (optional):
After you drop your png file into Jmol, and see your molecule, and before you set theplayback speed and generate the .gif file, you may resize the Jmol window if you wish.
The animation .gif file will be the same size as the window. You may also rotate themolecule to a different starting orientation, or zoom it (mouse wheel, or hold down
Shift while dragging up/down).
Making other rocking angles or playback speeds (optional):

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The files playback....spt contain Jmol commands that set the frame capture rate andplayback speed. If you wish, you can try other values by duplicating one of these files
and editing it with a plain text editor.
The files rock....spt contain Jmol commands that determine the rocking angle. If youwish, you can try other angles by duplicating one of these files and editing it with a plain
text editor. Note that the value at the end of the rock command is half of the full sweep
angle.
Smoother Rotation
Most of the animation script files move 1 degree between frames. If this seems toojerky, you can try moving 0.5 degree between frames at the expense of doubling the size of theGIF file produced. Try rotateslab-rock-y-60-0.5deg.spt. Although it is named "rotateslab" it will
equally well rock a view that has no slab cuts.
Animating a slabbed view including Density Maps
Slabs: There are two kinds of slabbing.
1. Most likely, you will want Rotate Slab mode: the cut faces will rotate with themolecule. This requires that you check "Rotate Slab" in the Slab dialog of FirstGlance
before saving your PNG/JMOL file. Rotate-slab example showing half of a virus
capsid. Choose a script such as slabrotate-y-60.spt, or another "slabrotate-....spt"
script file. It will produce a rotateslab....gif output file that you should immediately
rename.
2. Less likely, you will want Rotate Through Fixed Cut mode: the molecule will rotate
through a cut plane that remains fixed parallel to the screen. Rotate-through-cut
example showing half of a virus capsid. Scripts, for example slab-back50-rock-y60.spt, are provided that will animate the entire back half of the molecule. Use thisfor Step 8 above. Step 7 is irrelevant as the script sets the playback speed (which youcould edit). Also, the slab settings in the png file are irrelevant since the script
applies slab settings to show the rear half of the structure. These slab.....spt script
files will produce a slabbed.gif output file that you should rename immediately.
Density Maps: Use slab-back53-rock-y-60.spt, or if you have changed the density map
slab setting to, for example, mid 6%, use slab-mid6-rock-y-60.spt. An example for the Xray Density Map of an isopeptide bond is 6vzx-rock-slabbed-mid10-y-60.gif
Verifying your Java version (optional):
You must be online to do this.
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A. In the Type here to search slot at the left in the Taskbar below your desktop, enter
control panel.
B. If you are viewing by Category, select Programs. If you are viewing by icons, skip thisstep.
C. Click on Java.
D. In the Java Control Panel that opens, select the Update tab. Click the Update Now
button at the lower right. It will tell you if you have the current version. If you don't,
proceed to update.
macOS:
A. Open System Preferences.app (in your Applications folder).
B. Click on Java in the bottom row. (If Java is not there, you don't have Java installed.
Go to java.com, download, and install.)C. In the Java Control Panel that opens, select the Update tab. It will tell you if you havethe current version. If you don't, there is a button for updating Java.

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