You might want to contact peisach at auriga.rose.brandeis.edu and ask about
RAYSCRIPT, which does exactly what you want:
molscript -> rayscript -> rayshade
Jim Head
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James F. Head, PhD e'mail jfh at medxtal.bu.edu
Professor of Physiology tel # (617) 638-4396
Structural Biology Group fax # (617) 638-4273
Department of Physiology
Boston University School of Medicine