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<div class="moz-cite-prefix">Hi,<br>
<br>
two things:<br>
<br>
- make sure the altlocs of the residue and water are non-blanc and
*different*. For example: set residue altloc to A and water altloc
to B (if you make then the same they will be pushed apart by
non-bonded repulsion term!); AND<br>
<br>
- make sure their occupancies are constrained during refinement
such that: occupancy(residue) + occupancy(water)=1. This can be
done either manually by defining constrained groups as described
in the documentation page below (preferred option) or make sure
the water and residue have the same chain id and residue number.<br>
<br>
Let me know if you have any questions or need any help with this!<br>
<br>
Pavel<br>
<br>
On 7/16/12 7:57 AM, Nathaniel Echols wrote:<br>
</div>
<blockquote
cite="mid:CALeAa1N4857adXEgwg4Extyp0MqBYc_RaLBXY4pv33QpWixvTA@mail.gmail.com"
type="cite">On Mon, Jul 16, 2012 at 1:08 AM, subhash bihani <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:subhashbihani@gmail.com" target="_blank">subhashbihani@gmail.com</a>></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">
In one of my structure I have to put some water molecule in
alternate<br>
confimation with amino acid residues and in another case with
ligand.<br>
How do I do it in Phenix.<br>
</blockquote>
<div><br>
</div>
<div>You just need to make sure the "altloc" identifier in the
PDB file is set correctly for the atoms of interest.
Currently this requires opening the file in a text editor,
but I hope to have a better solution available very soon. The
water molecule should have the same altloc as the amino acid
residues which you want it to interact with - that is, if you
set the altloc for the residues to A, the water also needs to
be A. You may want to constrain the occupancies to be the
same; see the manual here:</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="https://www.phenix-online.org/documentation/refinement.htm#anch111">https://www.phenix-online.org/documentation/refinement.htm#anch111</a></div>
<div><br>
</div>
<div>-Nat<br>
</div>
</div>
</blockquote>
<br>
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