From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 12 2011 - 12:53:39 CDT

Hi,
  Michell Kuttel and Simon Cross developed the code to compute the
pucker parameters, so they are the best people to ask for a succinct
explanation. If you want to see the code however, it is in the
VMD source file DrawRingsUtils.C, which I link to below:
http://www.ks.uiuc.edu/Research/vmd/doxygen/DrawRingsUtils_8C-source.html#l00102

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 07, 2011 at 01:35:18PM -0600, Payne, Christy wrote:
> I have written a VMD tcl script to obtain the pucker parameters for a six-member ring over the course of a trajectory. I have a couple of questions regarding what I get back.
>
>
> 1. Are these parameters still obtained using the Hill-Reilly methodology? [using $sel get pucker]
> 2. How are the three Hill-Reilly angles describing canonical ring pucker conformations combined to obtain a single parameter?
>
> Thanks!
> Christy

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