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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Dear Eric
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<div>I had a similar case. Apart from giving them the same residue number and "A" and "B" altloc identifiers, you should <span style="font-size: 10pt;">make sure the summation of their occupancies equals 1. Therefore you can use the "occupancy refinement selections"
(in the GUI, go to "all parameters", then "atoms selections") and select your two ligands as "constrained groups".</span></div>
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<div>Kind regards</div>
<div>Elke</div>
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<div id="divRpF465906" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>Van:</b> phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] namens Nathaniel Echols [nechols@lbl.gov]<br>
<b>Verzonden:</b> woensdag 30 juli 2014 22:00<br>
<b>Aan:</b> Eric Girard<br>
<b>CC:</b> PHENIX user mailing list<br>
<b>Onderwerp:</b> Re: [phenixbb] Two ions at same position<br>
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<div dir="ltr">They need to have the altloc identifiers set differently: one ion gets "A", the other gets "B", which will prevent them from clashing in refinement. It is probably a good idea to give them the same residue number if you haven't already - I'm
hoping this will result in the occupancy constraint being handled automatically.
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<div>-Nat</div>
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<div class="gmail_extra"><br>
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<div class="gmail_quote">On Wed, Jul 30, 2014 at 3:53 PM, Eric Girard <span dir="ltr">
<<a href="mailto:eric.girard@ibs.fr" target="_blank">eric.girard@ibs.fr</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
Dear phenixbb members,<br>
<br>
I am refining a structure that contains Ca2+ atoms. The structure was determined in presence of lanthanide ions. Thus, the resulting density clearly indicates that a part of each Ca2+ sites is substituted with Eu3+ (let's say 75% Ca2+ and 25% Eu3+ per sites).<br>
How can I deal with such situation? Indeed phenix.refine complains when I try to put a Ca2+ ion and a Eu3+ one with the same coordinates (and with the occupancies mentionned above) and stop.<br>
<br>
Thanks for your help.<br>
<br>
Eric.<br>
<br>
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