[phenixbb] Two ions at same position

Nathaniel Echols nechols at lbl.gov
Wed Jul 30 13:00:30 PDT 2014


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 at 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
>
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