they are drawn in different positions, between different atoms. "sidechain"
means directly between the O and the N, for instance, in a peptide. "backbone" means between the alpha carbons. Since the lines are actually in different locations, I thought a new calculation was required. To me that's not quite the same as only a change in rendering. It requires a more sophisticated analysis (I thought.) Anyway, that's what I meant.
Miguel wrote:
The problem is that "backbone" and "sidechain" in "set hbonds" is a fundamental characteristic of how hbonds are calculated, not how they are displayed.
Bob, I don't understand what you are saying ... I must be missing something.
The 'set hbonds/ssbonds sidechains/backbone' statements only control how the bonds are rendered ... they do not affect calculations.
Please advise.
Miguel
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