Creating Movies

Jmol / JSmol Tutorials

• A list of Jmol / JSmol Tutorials written by users.
• Using the mouse (English · Español · Français · Japanese).
• Scripting quickstart: rendering options · selecting atoms.
• How to create surfaces and isosurfaces, including cavities, pockets and tunnels.
• Displaying shapes, polyhedra, orbitals, dipoles, distances, forces and vibrations.
• Creating movies.
• Customizing Jmol: macros · menus.
• Web pages without writing code by using the Jmol "Export to Web" function.

This section is about making true movies. A true movie is a series of images played in sequence. Unlike a "live" animation in Jmol, if all you have is the movie, you cannot use the mouse to rotate the molecule to watch the movie from different perspectives, nor can you change the color scheme or rendering of the molecule.

There are several possible advantages to true movies. Jmol may be unable to render large complex animations fast enough to avoid a slow, jerky appearance. Transparency and large spheres, especially at high quality (set antialiasdisplay on) are some of the renderings that are slow. Capturing Jmol's renderings as a movie enables much faster playing, e.g. 24 frames per second. Another advantage is that the movie can be shared as a single file, and kept private, in situations where one does not want the animation on a public website, and when the recipient is not familiar with using the stand-alone Jmol application.

Jmol can create a series of jpg, png, or gif images. There is currently no menu option to do this, but a small bit of scripting can do the trick. It is possible to get the movie output from either one frame at several angles or from a series of frames. The images can then be assembled into a single file that will play as a movie.

Image/Movie Size

Normally you simply adjust the size of the Jmol application window to the desired size before writing the image files. If you want an exact size, such as 640 x 480 pixels, you can set that easily. Open Jmol's Display menu and select Resize. If you want an image larger than you can achieve by resizing your window using a mouse, it can be set using the Display, Resize method. You may not be able to see the entire Jmol window on your screen if you set a large size, but the images will be saved at the desired size (for example 1024 x 768 pixels).

Movies from trajectories

Trajectories read in as multiple files

If the trajectory is a series of files read in as 1.0, 2.0, 3.0, etc., the following will work:

 write frames {*} 800 600 "all.jpg" 

Trajectories from a single file

Often, the trajectory is one big file with consecutive frames. Read it in with e.g.:

 load trajectory "filename.xyz" 

create a script "trajectorymovie.jmol"

 frame 1
 num_frames = getProperty("modelInfo.modelCount")
 for (var i = 1; i <= num_frames; i = i+1)
   var filename = "movie"+("00000"+i)[-4][0]+".jpg"
   write IMAGE 800 600 JPG @filename
   frame next
 end for

then perform

 script "trajectorymovie.jmol"

Alternative approach (e.g. in pre-11.7 Jmol)

The main part of the script is given here: based on a mail from Bob Hanson on the mailing list. If you want to rotate a single molecule, you need to uncomment the respective 'rotate' commands. If you want to loop over the timeframes in your coordinate file, you only need to change the 'nFrames' variable to the amount of frames you are currently using (this is given in the title of the main Jmol window). You might also want to change the width and height parameters to create a bigger or smaller animation.

name = "./frame0000.jpg";
nFrames = 125;
nDegrees = 1;
thisFrame = 0;
width = 640;
height = 480;

set zoomLarge false;

message loop;
thisFrame = thisFrame + 1;
fileName = name.replace("0000","" + ("0000" + thisFrame)[-4][0]);
#rotate x @nDegrees;  # use these options if you want to rotate the molecule
#rotate y @nDegrees;
#rotate z @nDegrees;
frame next; # only use this if you have a multiframe file.
refresh;
write image @width @height @fileName;
if (thisFrame < nFrames);goto loop;endif;
background black;

Save this text in a file, for example 'movieloop.jmol'.

Alternative example

This uses the same principles, slightly different (though equivalent) code and is set for the rotation of the model in a single frame. In addition, it exports to gif format (only available in recent 11.7 versions) for later making an animated gif file outside Jmol:

load whatever_file.mol
color background [xD2DFEF]
/*
  add any other rendering commands
*/
for (var i=0; i<36; i=i+1)
  write image 200 200 @{"movie" + ("0000" + i)[-3][0] + ".gif"}
    /* 200 and 200 are width and height */
  rotate axisangle {1 1 0} 10
    /* axis is defined by X Y Z lengths between braces; this one is at 45 degrees
      and 10 (degrees) is angle of rotation, so the 36-loop gives a full turn
    */
end for

Viewstate

Now you still need to create a viewstate for the initial display. To do this, load the system coordinates you are interested in, rotate and change background colors until the picture looks as you want it. This can be saved into a file with the command:

write state "moviestate.jmol"

A state file looks something like this (only some of the important parts are shown):

...
load "CoCr_125frames.XYZ";  # This part is essential!
...
cameraDepth = 3.0;
center {6.424099 3.137966 4.133584};
moveto /* time, axisAngle */ 0.0 { -704 -672 -228 173.73} /* zoom, translation */  62.1
2 0.0 0.06  /* center, rotationRadius */ {6.424099 3.137966 4.133584} 9.94055;;
slab 100;depth 0;
...

Creating images

• Linux console:

To create the animation, make a file with first the viewstate and then the loop, for example by:

cat moviestate.jmol movieloop.jmol > movie.jmol

jmol movie.jmol

• Jmol console (any OS):

Start Jmol, open the script console, and type:

script moviestate.jmol 
script movieloop.jmol 

Jmol will start, and show you the animation, while it is writing the output files.

Converting images to a playable movie

Apple Mac OS X

Quicktime Pro is an easy and inexpensive program that can assemble a series of jpg files into movies in various formats (mp4, avi, wmv, etc.). The free version of Quicktime does not do this job -- you will need to buy a license for the Pro version.

Even if you are using Lion (which comes with Quicktime 10), you should install Quicktime 7. It is easy to find many complaints about Quicktime 10 online. In contrast, using Quicktime 7 is straightforward and it performs well. If your OS X came with Quicktime 10, you can also install Quicktime 7 and use either one that you choose for a particular use.

Assembling the Movie

Loading the Image Files

You must create, with Jmol, a series of sequentially numbered jpg image files, all in the same directory. For example m1.jpg, m2.jpg, ... m360.jpg for a 360 degree rotation in one-degree steps. In Quicktime, open the File menu, and select Open Image Sequence .... Select only the FIRST jpg file in the series (or actually any file in the series). Quicktime does not allow you to block select the range of files to be included in the movie. Therefore the directory containing the first file must contain exactly the files you wish to include -- you cannot select a subset of those files.

Once the series of image files loads, you will be asked to select a frame rate, for example 10, 15, or 24 frames/second. Then you can play the movie (but it has not yet been saved).

Saving the Movie

Open the File menu and select Export. In the Export: menu, pick an export format such as MPEG-4 (mp4), AVI (avi), or Windows Media (wmv). (See more about each format below.) After you have set the correct Options (see below), click the Save button and your movie file will be created.

MPEG-4

MPEG-4 (mp4) format will play in Quicktime (including free Quicktime) without complications on Macs, either as a stand-alone mp4 file (double click it), or embedded in a web page using the Quicktime browser plugin. Windows users will need to install free Quicktime.

A good quality mp4 movie of size 1024 x 768 pixels, with a reasonable file size (1.9 megabytes for 360 frames) was obtained with the following options (click the Options button, and use the Video tab):

• Video format: H.264
• Data rate: 1024 kbits/sec
• Optimized for: CD/DVD-ROM
• Image size: Custom, 1024 x 768
• Preserve aspect ratio (NOT checked)
• Frame rate: 24
• Key frame: Automatic
• Video options:
  • Restrict profiles to: Main
  • Encoding mode: Best quality (multi-pass)

Linux

Encoding to the mpeg format

The most straightforward way to encode to mpeg2 in Linux systems is "convert". This will create huge files and the needed mpeg2encode might not always be installed.

convert *.jpg movie.gif
convert *.jpg movie.mpg

Alternatively, encode to smaller mpeg4 files with mencoder, which comes along with mplayer.

Many options and codecs are available, the default settings often create images that are too grainy due to the high image compression. Some testing by Mario Valle at CSCS gave optimal mencoder options for a movie of atomistic simulations. To have it run on default Windows installations (e.g. for use in Powerpoint), also use the msmpeg4v2 codec with autoaspect. The optimal combination of mencoder options then becomes:

mencoder "mf://*.jpg" -o movie.avi -ovc lavc -lavcopts vcodec=msmpeg4v2:autoaspect:vbitrate=2160000:mbd=2:keyint=132:vqblur=1.0:cmp=2:subcmp=2:dia=2:mv0:last_pred=3 -fps 8

If the movie has just to be played on linux, one can also just type:

mencoder "mf://*.jpg" -o movie.avi -ovc lavc -fps 8

Fine tune the speed/length of the animation by varying the -fps (frames per second) option.

Encoding to animated gif format

Animated gif, also called multi-gif, is an older format that plays in all major web browsers without installing any special plugins. You will need a third-party software for this. E.g. gifsicle. Load into it the full set of gif files generated by Jmol (gif format is only available in recent 11.7 versions of Jmol), choose the time step and the loop options and save into animated gif.

Contributors

EricMartz, Pimpim, NicolasVervelle, Fuse809, AngelHerraez