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.

An animation is just a sequence of images, so all one needs is Jmol to create a batch file of 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.

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 an inexpensive way to 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 come 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.

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