How to View/Create animations with Molden

Viewing animations

Why should you want animations when you already have molden ? For one thing you can create animations to be used in a WEB tutorial. Secondly, for large molecules such as proteins the solid drawing mode is prohibitively slow. These Molden pages use two kinds of animations; gifanim and fli. The gifanim animations are handled by the NetScape browser. On an Xwindows platform fli can be viewed with xanim. xanim is a program for viewing a wide variety of animation formats under X11. To have animations automatically displayed from a WWW browser read about MIME types.

You should now be able to watch the following animation:

Creating animations with Molden

With the latest version of Molden it is also possible to create animations. I have never succeeded in making a decent mpeg animation of a series of gif files, therefore I restrict myself to two types of animations: , .fli and gifanim, for both you'll need some additional software.

.fli animations

Additional software needed:

• The FBM2FLI program and the FBM package , since you need the FBM libraries to build FBM2FLI. (See also The FLI/FLC animation format). fbm2fli will let you create an fli animation from a series of GIF images.

Here is in short a session for creating a fli animation:

• The latest version of Molden has the built in capability to write gif's.

• Start Molden, load in a file and click the button from the Molden Control Window when you are ready to start the animation.

• Now every time the main window is updated a GIF picture of it with the name mol*.gif is created, where * is the sequence number. Molden will not create more than 1000 GIF pictures.

• Clicking the button again, will stop the generation of GIF pictures.

• Now exit Molden.

• You might inspect/downsize the series of gif images with a program like xv.

• Create a list-file say mol.txt for fbm2fli. This is a file which lists per line the next gif file to be used in the animation. (On UNIX: \ls -1 mol*.gif > mol.txt).

• Execute fbm2fli by typing: "fbm2fli mol.txt mol.fli".

• View the animation by typing "xanim mol.fli".

Using fli animations in your own WWW HTML pages

Your WWW server has to know about fli animations. Add the following line to the file mime.types in the servers conf directory:

video/fli                      fli

gifanim animations

A gifanim actually uses the GIF89a format, which allows multiple gifs to be stored in one file along with the information of how many times the animation should be looped. Only the NetScape browsers support this type of animations. (See the GIF Animation Home Page).

Hoe to create a gifanim with molden:

• Generate a series of .gif's with molden, see above.

• Generate a GIF89a file with the help of the Whirlgif program.

  whirlgif -loop 1000 -globmap -o t.gifanim *.gif

• You can include the gif in your HTML page like you would include a normal gif.

  <IMG SRC="pictures/peravib.gif">

NOTE: Use the molden commandline flag -l if you dont want the molden logo in your animation.

VRML2.0 animations

Molden can create two types of VRML 2.0 animations:

• The molecular structure animations.

  This presumes you read in an Gamess/Gaussian optimization/saddle run or an xyz file containing multiple structures:

  • Start molden with the -w 3 commandline option:

    molden -w 3 ampac.arc

  • Select solid or stick drawing mode from the molden control window.

  • Hit the movie button, at the end molden will say: wrote file: movie.wrl.

  • Read in to an VRML2.0 compliant browser (eg: cosmoplayer). Click on any of the atoms in the scene to start the animation. Click Here to view a VRML2.0 animation.

• Animation of molecular orbitals or electron density as a molecule undergoes a reaction.

  The latter can only be accomplished by doing a series of single point calculations on separate points of the reaction path, for each of these points you must write out a VRML2.0 file. You can combine these VRML2.0 files into one VRML2.0 files with the following script

  (Usage: multi_vrml_orbitals.csh vrmlfile1.wrl ... vrmlfilen.wrl).

  You can watch an orbital change shape as the molecule undergoes a reaction Here (Click on the orbital to start the animation) (This is a big file 4MB and it will take quite some time to interpret as well).