Subject: Unrolled helix diagrams

From: "G. Ravishanker" <[email-masked]>
Date: Thu, 31 Mar 1994 11:44:13 -0500

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:[email-masked]  *
* Middletown, CT 06457.                                                    *
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