Hello everyone, I am in the final rounds of refining my protein at high resolution and currently trying to model an alternative conformation of a Chl /a/-phytol chain. I inserted a second phytol chain with coot - worked out well so far (alternate chain identifiers A and B for both phytol chains). After using phenix.refine, however, the occupancy of the second phytol chain was refined to 0. When splitting the whole Chl molecule the occupancy refines to sensible values (0.34 and 0.66). We would prefer to only model the phytol chain in alternate conformation as the macrocycle superpose perfectly. Any suggestions regarding the occupancy problem? Another issue concerns restraints. We tried to turn of specific nonbonded restraints and found a phenixbb message from 2007: http://www.phenix-online.org/pipermail/phenixbb/2007-September/011734.html Are there any news/updates on this matter? Any help appreciated! Thanks, Moritz -- Moritz M. Machelett Ruhr University Bochum Protein Crystallography, Department of Biophysics, ND04/396 44780 Bochum Tel: +49-(0)234/32-25754