Since the release of Adobe Systems' Portable Document Format (PDF) version 1.6 in 2004, it has become possible to view interactively three-dimensional models that are embedded into PDF files. This attribute will dramatically increase information content as well as data transparency in scientific papers. Additionally, replacing multiple two-dimensional figures of a three-dimensional structure with one integrated interactive three-dimensional model will reduce the need for supplementary material.
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Murienne et al. (2008) studied this question.