On Wed, Apr 7, 2010 at 4:48 PM, Pavel Afonine <span dir="ltr">&lt;<a href="mailto:PAfonine@lbl.gov">PAfonine@lbl.gov</a>&gt;</span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">



  

<div bgcolor="#ffffff" text="#000000">rigid body refinement does not employ any restraints. You can use
secondary structure restraints in refinement of individual coordinates.
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Actually, you can use secondary structure restraints in constrained
rigid body refinement (SA in torsion angle space).<br></div></blockquote><div><br></div><div>I&#39;m not sure to what extent this is true.  Ralf, what would be the effect of those extra H-bonds when running torsion angle dynamics?  Will they be used in the rigidity analysis, or will they just behave as they would in cartesian dynamics?</div>
<div><br></div><div>-Nat</div></div>