Re: [phenixbb] Two ions at same position

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 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: [email protected] [[email protected]] namens Nathaniel Echols [[email protected]] 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. -Nat On Wed, Jul 30, 2014 at 3:53 PM, Eric Girard mailto:[email protected]> 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. -- **************************************************************** 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 45tel:%2B33%20%280%294%2057%2042%2086%2045 Fax: +33 (0)4 76 50 18 90tel:%2B33%20%280%294%2076%2050%2018%2090 Web site: http://www.ibs.fr/ ***************************************************************** _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb