Unrolled helix diagrams

["G. Ravishanker" <ravishan "at@at" swan.wcc.wesleyan.edu>]

 Hi
 I am trying to generate the unrolled-helix diagrams that you see in some
 of the DNA papers, especially the ones from Dickerson's lab. It is
 basically a cylindrical projection of the backbone (or even the bases, if
 one wants) whereby one projects all DNA atoms to a cylinder of particular
 radius and then cut open the cylinder. The 2-D projection typically has
 the polar coordinates (the angle phi and the z-coordinate) plotted against
 one another. I am having problems carrying this out:
         1. After the projection, when I draw the unrolled structure (in
            2-D), some parts of the backbone are phase-shifted. That is,
            the backbone does not appear as a single line, but as a line of
            some n-bases and then the next contiguous bases on the same
            helix appear as another line shifted by 180. I have
            managed to correct this by some "ugly" piece of code.
         2. The distance in the 2-D diagram between the phosphates of the
            two helics do not correspond to the 3-D distances. This is of
            course a major problem. Since one of the axes is an angle and
            the other a distance, what exactly should be done to reflect
            the 3-space geometry correctly in 2-space?
 I would appreciate any help I can get and Thanks in advance.
 Ravi
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 * Ganesan Ravishanker			Ph: (203) 344-8544 Ext. 3110       *
 * Coordinator of Scientific Computing,  Fax:(203) 344-7960                 *
 * Adjunct Associate Professor(Dept. of Chem.)                              *
 * Wesleyan University               e-mail:ravishan "at@at"
 swan.wcc.wesleyan.edu  *
 * Middletown, CT 06457.                                                    *
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