[phenixbb] occupancy refinement

Nicole Bischoff nbischoff at bioc.unizh.ch
Wed Jan 28 00:35:41 PST 2009

Dear all,

in my electron density I can see negative difference density (fo-fc) for 
the carboxyl groups of some aspartates or glutamates. Assuming that this 
is a result of partial decarboxylation due to radiation damage, I wanted 
to refine the occupancies of these carboxyl groups.

To this end, I set the occupancy of these atoms to 0.99 in Coot so that 
they would be picked up by occupancy refinement in phenix.refine (using 
version 1.4-3). Phenix however just  put the value back to one.  It 
looks like the occupancy refinement in phenix is meant for alternative 
conformations where the sum of the occupancies of the different 
conformations is 1.

How can I make phenix refine partially decarboxylated acidic side 
chains? It does not seem appropriate to me to make alternative 
conformations, one with and one without the carboxyl group. That would 
look funny at my resolution (2.7 Angstrom) and might not fix the problem.

Any hints are appreciated.

Thank you,


Nicole Bischoff, M. Sc.
PhD student in the Gruetter lab

Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
8057 Zurich

+41 44 635 5556
nbischoff at bioc.unizh.ch

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