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.

-Nat

On Wed, Jul 30, 2014 at 3:53 PM, Eric Girard <eric.girard@ibs.fr> wrote:

Dear phenixbb members,

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).
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.

Thanks for your help.

Eric.

--
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Eric Girard

Extremophiles and Large Macromolecular Assemblies (ELMA) group

Institut de Biologie Structurale
UMR 5075 CEA-CNRS-UJF-PSB
71 avenue des Martyrs
CS 10090
38044 Grenoble Cedex 9

Phone: +33 (0)4 57 42 86 45
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Web site: http://www.ibs.fr/

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