Use different altloc tags in the PDB (Column 18). For example:<br><br><pre>HETATM 2142 O AHOH 1009 1.332 -11.668 14.957 0.50 6.57 O <br>HETATM 2143 O BLIG 1010 7.403 -7.755 -0.773 1.00 29.28 O <br>
</pre>Then it will know they don't occupy the same space at the same time. As a word of warning the occupancy refinement of two proximal atom that don't have the same residue number can sometimes add up to more than 1 so check to make sure the model makes physical sense.<br>
<br>Hope this helps,<br><br>Katherine<br><br><div class="gmail_quote">On Mon, Mar 28, 2011 at 2:40 PM, Brandon Goblirsch <span dir="ltr"><<a href="mailto:gobli033@umn.edu">gobli033@umn.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hello,<br>
<br>
Currently I am have a structure which has a ligand bound at less than<br>
full occupancy. �The ligand in this cause is covalently linked to a<br>
CYS residue in the enzyme active site. �When the ligand is not<br>
present, there are two well conserved waters in the active site in its<br>
place. �Overall, I have a same space, split occupancy issue. �The<br>
problem I am having now in phenix 1.7.460 is that I want to refine<br>
(simultaneously) these water positions superimposed on the bound<br>
ligand position (as both have less than 100% occupancy). �However,<br>
upon refinement, the waters are always "kicked out" of position and<br>
are not allowed to overlay with atoms within the bound ligand. �Does<br>
anyone know how to get phenix.refine to accept the water and ligands<br>
occupying the same coordinate space. �Obviously setting the ligand and<br>
water positions to sub 100% occupancy does not do the trick.<br>
<br>
Thanks for any help!!<br>
<br>
Brandon<br>
--<br>
Brandon Goblirsch<br>
Research Assistant-Wilmot Lab<br>
Biochemistry, Molecular Biology and Biophysics<br>
5-230 Nils Hasselmo Hall<br>
Minneapolis, MN 55455<br>
<a href="tel:%28612%29624-0141">(612)624-0141</a><br>
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</blockquote></div><br>