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Perspective/Orthographic views
In the perspective view (the default), objects which are far away are
smaller than those nearby. In the orthographic view, all objects
appear at the same scale. Since some prefer one over the other, both
options are available. Perspective viewpoints give more information
about depth and are often easier to view because you use perspective
views in real life. Orthographic viewpoints make it much easier to
compare two parts of the molecule, as there is no question about how
the viewpoint may affect the perception of distance.
vmd@ks.uiuc.edu