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Hi Nat,<br>
<br>
the way it's implemented currently: you can't add constraints on top
of another constraints. I'm not aware of any existing program that
can do it, although technically it's easy to implement. <br>
<br>
However, Dalibor can do what he wants (if I understand two previous
emails correctly). In fact, phenix.refine will do it automatically,
so there is no need to even do anything special.<br>
<br>
Pavel.<br>
<br>
<br>
<br>
On 11/25/10 11:08 AM, Nathaniel Echols wrote:
<blockquote
cite="mid:AANLkTikPwEi1WPcZkwHj0s9O6XThFR--bEqUEFcnHL+-@mail.gmail.com"
type="cite">On Thu, Nov 25, 2010 at 10:26 AM, Pavel Afonine <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>></span>
wrote:<br>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
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 "AGLU A 30 " = occupancy of
"AALA A 451 ", 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'm confused too - isn'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 = "chain A and resseq 30"</div>
<div> selection = "chain A and resseq 451"</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>
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