[Chimera-users] Cartoon: Helix appearance

kroneml at hotmail.de kroneml at hotmail.de
Thu Oct 25 15:47:43 PDT 2007


I observed that Chimera (like almost all other protein viewers) aligns the
ribbon of a helix in a way that the ribbon is parallel in every twist (the
ribbon virtually forms a cylinder).
My question is: is this correct, strictly speaking? I thought that the
ribbon should lie in the plane defined by two successive C-alpha atoms and
the associated O atom? (Mike Carson defines it that way in his "Ribbons",
following the instructions of Richardson's "The anatomy and taxonomy of
protein structure"). If you draw it that way, the ribbon forming the helix
will tilt slightly outwards.
Is the alignment of the helix ribbon in Chimera done simply because it looks
better this way or is there another reason?

I did some research on this topic via google and even asked a certified
biologist (scientific assistant), but the internet had not much to say about
it and the biologist only told me that cartoon drawings don't have to be
very accurate, since they are only a tool to get a general idea of the
protein's structure.

Best regards,
Michael Krone

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