Animate molecular vibrations as multiple xyz coordinate files I have a frequency calculation by Gaussian09. Now I would like to extract vibrational modes as a set of xyz coordinate files. I would like to manually recompute numerically the points along a transitional vector, since IRC calculations all fail. (I suspect it is no real saddle point, flat PES.)

Consider the formation of the Lewis-Acid-Base complex $\ce{H3N\bond{-}BF3}$ with a transition state given in $$\ce{NH3 + BF3 -&gt; [H3N\cdots BF3]^{TS} -&gt; H3N\bond{-}BF3}$$ where this procedure would equal a (rigid) scan of the $\ce{N\cdots B}$ bond. This would be easy to accomplish.

Things get more difficult considering the pseudo vibration of ammonia, pyramidal to planar to pyramidal. Here it is not only one variable that has to be changed. (With dummy atoms it is still manageable.)

If molecules get more complicated, the manual specification of the bond parameters is too complicated and a source of many errors.

In the days when some of the gui programs were not able to calculate the vibrations and showing them in that fashion it was common to produce a set of multiple xyz files, each of them a snapshot of the coordinates along a specified vibrational vector. (This is now done internally and you can look at fancy pictures.) One of those programs capable of doing so is XVibs. For various quantum chemistry packages they calculated the distorted geometries. Unfortunately that is now ancient. (It was possible with a Gaussian09 output.) 

For Turbomole there is a tool distributed along called screwer.

Unfortunately I have no access to that program package and I also do not want to change all the computations so far done to this software.

Lordstryker already posted in the comments, that it might be done by hand with chemcraft. I tried that and it is not very satisfying. One produces too many errors.

Are there any other programs/scripts that might be able to produce these files?
If I remember correctly, frequency data are in the stdout clusterfuck usually named log file, as well as in the (formatted) checkpoint files. There shouldn't be any need to prepare a cube file for this.

If GaussView is not available, GM's comment has the answer: Avogadro can visualize vibrations and I'm sure I've done this. Unfortunately, I don't have an output file at hand here.