On Thu, Nov 25, 2010 at 10:26 AM, 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 text="#000000" bgcolor="#ffffff">In the example below I see residue #30 has two conformations, A and
    B, and they are automatically constrained-refined in phenix.refine
    and their sum adds up to 1 (0.52+0.48).<br>
    Same for residue #451.<br>
    <br>
    Although I see that occupancy of &quot;AGLU A 30
    &quot; = occupancy of &quot;AALA A 451
    &quot;, it is not guaranteed in refinement, since otherwise that would be
    a double-constrained refinement:<br>
    <br>
    constraint #1: occupancy(AGLU A 30) + occupancy(BGLU A 30)=1
    <br>
    constraint #2: occupancy(AGLU A 30) = occupancy(AALA A 451)<br>
    <br>
    which is not currently available. <br></div></blockquote><div><br></div><div>Wait, now I&#39;m confused too - isn&#39;t this the entire point of the constrained_group setting?  For example, the parameters below:</div>

<div><br></div><div>refinement.refine.occupancies.constrained_group {</div><div>  selection = &quot;chain A and resseq 30&quot;</div><div>  selection = &quot;chain A and resseq 451&quot;</div><div>}</div><div><br></div><div>

If both selections have alternate conformers A and B, and the occupancies for A and B are both 0.5, what would phenix.refine do?</div><div><br></div><div>-Nat</div></div>