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--></style><title>Re: [phenixbb] grouped occupancy
definitions</title></head><body>
<div>Ralf,</div>
<div><br></div>
<div>Pavel's working on a suggestion (he's sick).</div>
<div><br></div>
<div>using altlocs I can see how to build group selections that tie
nonadjacent residues together, since occupancies for ACS within
residues are constrained to 1.0, but I'm not sure if these is best
way. It gets</div>
<div>tricky when waters join the group.</div>
<div><br></div>
<div>e.g</div>
<div><br></div>
<div><font face="Courier" color="#000000">constrained_group
{</font></div>
<div><font face="Courier" color="#000000">selection = chain A and
resseq 2</font> and altloc A</div>
<div><font face="Courier" color="#000000">selection = chain A and
resseq 21</font> and altloc B</div>
<div><font face="Courier" color="#000000">}</font></div>
<div><br></div>
<div>takes care of non adjacent residues, but then when I add a group
containing a water</div>
<div><br></div>
<div><font face="Courier" color="#000000">constrained_group
{</font></div>
<div><font face="Courier" color="#000000">selection = chain A and
resseq 2</font> and altloc A</div>
<div><font face="Courier" color="#000000">selection = chain S and
101 </font> and altloc B</div>
<div><font face="Courier" color="#000000">}</font></div>
<div><br></div>
<div>how will phenix parse the combined groups ?</div>
<div><br></div>
<blockquote type="cite" cite>Did Pavel reply to this already?<br>
<br>
> 1) How do I select ACs<br>
</blockquote>
<blockquote type="cite" cite>altloc A<br>
<br>
> 2) How do I constrain water occupancies so that their Q + that
of<br>
> coupled protein atomes does not exceed 1. If I match
the AC flags<br>
> for the waters and side chains will this take care of it.<br>
<br>
Not if they are in different residues; but it is important to
match<br>
the altloc characters to get meaningful nonbonded interactions.<br>
You need to use Pavel's occupancies.constrained_group selections
in<br>
addition. I hope Pavel will give you the details on those.<br>
<br>
Ralf<br>
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<div><br></div>
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