[phenixbb] Two ions at same position

Elke De Zitter Elke.DeZitter at chem.kuleuven.be
Sat Aug 2 05:36:45 PDT 2014

Dear Eric

I had a similar case. Apart from giving them the same residue number and "A" and "B" altloc identifiers, you should 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".

Kind regards

Elke De Zitter

PhD student, KU Leuven

Biochemistry, Molecular and Structural Biology

Celestijnenlaan 200f - bus 2404, 3001 Leuven

Room 00.84, +32 16 3 26530

Van: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] namens Nathaniel Echols [nechols at lbl.gov]
Verzonden: woensdag 30 juli 2014 22:00
Aan: Eric Girard
CC: PHENIX user mailing list
Onderwerp: Re: [phenixbb] Two ions at same position

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.


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

Extremophiles and Large Macromolecular Assemblies (ELMA) group

Institut de Biologie Structurale
71 avenue des Martyrs
CS 10090
38044 Grenoble Cedex 9

Phone:  +33 (0)4 57 42 86 45<tel:%2B33%20%280%294%2057%2042%2086%2045>
Fax: +33 (0)4 76 50 18 90<tel:%2B33%20%280%294%2076%2050%2018%2090>
Web site: http://www.ibs.fr/


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