[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
----
Nicole Bischoff, M. Sc.
PhD student in the Gruetter lab
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
8057 Zurich
Switzerland
+41 44 635 5556
nbischoff at bioc.unizh.ch
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