Many aspects of these images were optimized for discerning the structures of the bilayers. The palmitic and oleic tails are given slightly different hues to help in discerning their positions. The bottom leaflet is darkened relative to the top leaflet, and the last carbons on the tails of the fatty acids in the bottom leaflet are white. One corner (16 PC's in each leaflet) is cut out, and the first two rows of PC's in the top leaflet are cut away. The waters associated with the top leaflet are cut away in front (x <= 7.0). Every second water molecule is deleted to allow seeing through the water cloud. Only the oxygens of the waters are shown, and at much less than actual spacefilling diameter (0.8A). The fatty acid tails are shown thinner than their actual spacefilling diameters, namely as wireframe 0.8A diameter, which leaves some space between them.
If you are interested in the PDB files or script which generated these views, ask.
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