Often when producing for the web sometimes we will encode to a lower frame rate. When choosing the new rate, there is one very important factor to consider. Be sure that the new frame rate will divide evenly into the old frame rate. For example if you have a 30 fps project that you want to encode to 10 fps, that would be okay. On the other hand if you tried to encode your 30 fps to 12 fps, it would appear choppy, because 12 does not go into 30 evenly. 
Another great way to improve quality when encoding with compressor, is to use frame controls. For example when trying to improve interlacing issues when encoding to Mpeg2, turn on the Frame Controls and change the Resizing controls to Best, Progressive, & Best. Adding these Frame Controls will also increase both output time, and Output size. However the improvement can be worth the increase in size.
As part of our 5 day Final Cut Studio class, we give an introduction to Apple Compressor. Understanding how and when to use Apple Compressor, is not always obvious.
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