I have created a mo graph video using After Effects and Premier in HD 1920X1080. The client wants a much smaller version in 320x240 but every time I render out the smaller version pixilates.
Is there a way I can fix this
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No matter what you try, you will lose quality as you are reducing the resolution significantly. So you are creating each new pixel from an aggregate of 36 - and depending on how you do that it can look okay or terrible, but it will not look anywhere near as good as the original. There is no way to avoid this.
Experiment with the settings for down sizing - for your video some may work better than others.