Hi. I&#39;m one of the Richardsons&#39; people. I have more experience with RNA, but have looked at DNA some as well.<div><br></div><div><span class="Apple-style-span" style="border-collapse: collapse; "><div>1. On C2&#39;-endo and C3&#39;-exo being equivalent: no, not quite equivalent, but related. If you do have C1&#39;, C4&#39;, and O4&#39; in the plane, then &quot;popping&quot; C2&#39; out on one side or C3&#39; out on the other is relatively similar (sort of) and there&#39;s a recognized &quot;twist&quot; conformation where you&#39;ve got them both out of plane a bit. However, you can really get C3&#39; mostly in-plane with the other three and have a conformation that&#39;s distinctly a C2&#39; endo pucker rather than looking like it could be either one. If you&#39;re building ideal B-form DNA, it would be better to use a real C2&#39;-endo pucker than the twist, and certainly better than using the C3&#39;-exo.&nbsp;</div>
<div><br></div><div>2. I&#39;m afraid I don&#39;t know the appropriate format for use with PHENIX, but there are pucker-specific parameters available on the Nucleic Acid Database site:&nbsp;<a href="http://ndbserver.rutgers.edu" target="_blank" style="color: rgb(0, 0, 204); ">http://ndbserver.rutgers.edu</a>&nbsp;-- specifically, here:&nbsp;<a href="http://ndbserver.rutgers.edu/standards/parameter.html" target="_blank" style="color: rgb(0, 0, 204); ">http://ndbserver.rutgers.edu/standards/parameter.html</a>&nbsp;-- these are set up for XPLOR, but the values should help. At any rate, these files distinguish the dihedrals for C2&#39;-endo and C3&#39;-endo sugar puckers. (The set for higher resolution also provides slightly different bond lengths and angles for them, since the ring strains are a bit different.) And I don&#39;t think they make a habit of turning up C3&#39;-exo.&nbsp;</div>
<div><br></div><div>Laura Murray</div><div><br></div></span></div>