We need to rotate the protein in a loop to by one degree and make a snapshot of each rotation step. You need to paste the following function in Tk console of VMD:

proc make_rotation_movie_files {} {
	set frame 0
	for {set i 0} {$i < 720} {incr i 2} {
		set filename [format "%04d" $frame]
		render snapshot $filename
		incr frame
		rotate y by 1
	}
}

Once we define this function, we can call it using:

make_rotation_movie_files

The files are saved in the current directory without any file extension. This is because I found that the function does not work correctly under GNU/Linux when you have it defined. In windows however, you can do the following:

proc make_rotation_movie_files {} {
	set frame 0
	for {set i 0} {$i < 720} {incr i 2} {
		set filename snap.[format "%04d" $frame].jpg
		render snapshot $filename
		incr frame
		rotate y by 1
	}
}

This generates 360 images for you with the tga format.

We need to retrieve the file extensions. In GNU/Linux run the following command in the folder with generated pictures:

ls -1tr * | while read filename; do mv $filename $filename.tga; ((counter++)); done

We need to convert these files to jpeg:

mkdir converted
ls -1tr *.tga | while read filename; do convert $filename converted/$filename.jpg; ((counter++)); done

And finally, we merge all of them to a gif file:

convert -fuzz 1% -delay 1x30 -loop 0 *.jpg -coalesce -layers OptimizeTransparency apoFinal.gif

If you want to decrease the gif size, do the following:

gifsicle -U apoFinal.gif --delay 3 `seq -f "#%g" 0 6 359` -O3 --colors 128 --scale .5 -o apoOptimized2.gif

Here you can remove some frames. This is what `seq -f "#%g" 0 6 359` does, it takes every sixth frame for final file. --colors decreases the number of colors and --scale scales with the factor written in front. Also -O3 optimizes the gif file as much as possible.

To do all these steps in windows, you can install VirtualDub software. Open first file and export as avi.