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What is needed?

vibs is a small Perl script that reads the optimized Cartesian coordinates and normal mode displacements from a Q.Chem or ACES output and generates a series of displaced Cartesian coordinates spanning one period/cycle of that normal mode. It is located at /usr/local/vibs.

Molekel is a molecular visualization program just like JMOL. It is used here because it can easily generate/export sharp images. It is located at /usr/local/molekel.

Makempeg is a simple shell script (that someone wrote) to take a series of JPEG files and turn them into an MPEG movie. It calls mpeg and ppmtoyuvsplit, which we have at /usr/local/bin.

Procedure
1. Use the script vibs to generate Cartesian displacement that get written to an XYZ file.

Example: To generate Cartesan displacements of the 12th mode from file freq.out, the commandline input would be
vibs freq.out 12
This generates a file called mode12.xyz

2. Open the newly generated Cartesian displacements file by running molekel. This is done by right-clicking and selecting the file through 'LOAD>MULTIPLE STRUCTURE XYZ'.

Once you orient the molecule into a certain position, right-click and select 'RENDER'. Set the parameters you want and make sure you select 'structure animation' in the 'action' section and click 'ok'.

In the next window, you would give a base name for the images that you would ultimately stitch into a movie.

3. Now comes the real movie-making part and we will use the makempeg script for that. You can type makempeg --help to view the usage information. Typically, if one generated 20 cartesian displacement using vibs and gave the basename basename in Molekel your commandline prompt would be

makempeg -fs 1 -fe 20 -fi 1 -base basename

This will generate a movie named basename.mpg. If something fails, you must be missing one of many executables (ppmtoyuvsplit, mpeg) that makempeg script uses.

Now you can see your movie using any movie player. A simple tool for Linux users would be plaympeg. To play a movie named basename.mpg in looping mode, your commandlike input would look like
plaympeg -l basename.mpg

What is needed?

vibs is a small Perl script that reads the optimized Cartesian coordinates and normal mode displacements from a Q.Chem or ACES output and generates a series of displaced Cartesian coordinates spanning one period/cycle of that normal mode. It is located at /usr/local/vibs.

Molekel is a molecular visualization program just like JMOL. It is used here because it can easily generate/export sharp images. It is located at /usr/local/molekel.

Gifsicle is a UNIX command-line tool for creating, editing, and getting information about GIF images and animations. We have it locally at /usr/local/bin.

Convert is a fairly standard part of the ImageMagick package that is used to convert between different image formats, JPEG to GIF in our case.

Procedure
1 - 2. The first two parts are the same as the above section.

3. Once you have your JPEG images, you would want to convert them into the GIF frames and then a GIF animation.

To convert the JPEGs into GIFs, you run
convert [options] *.jpg *.gif

Once you have all your GIF frames, you can use Gifsicle to stitch them together into an animation.
gifsicle --loop *.gif > animation.gif

You can automate the process using a simple Perl script like this one.

#!/usr/bin/perl -w
#######################################################
# Makes GIF animations
# 'convert' converts the JPEGs to GIFs
# 'gifsicle' joins the GIFs into an animation
#

chomp(@files=`ls *.jpg`);
foreach (@files){
$i=1;
if (/.jpg/){
$filename=$`;
} else{
print "No JPEG files found. \n";
exit;
}
system("convert -resize 600x600 $_ $filename.gif");
$build[$i]="$filename.gif ";
$i++;
}
print @build;
#system("gifsicle -b --transparent '#000000' *.gif");
#system("gifsicle @build --delay=100 --loop > animation.gif");
system("gifsicle --loop *.gif > animation.gif");