[phenixbb] Issue with SeMet residues

Mark Wilson mwilson13 at unl.edu
Thu Nov 7 13:12:34 PST 2013

Dear PHENIX users and developers,
I am refining a structure containing SeMet residues at atomic (1.05 Å)
resolution.  The model was initially refined in Refmac5 and behaved as
expected (i.e. reasonable R factors and agreement with maps).  I've used
this final Refmac5 model as a starting point for refinement in PHENIX
1.8.4 with standard settings, as below.

phenix.refine data.mtz \
refinement.input.xray_data.labels="F, SIGF" model.pdb \
 main.use_experimental_phases=false  \
 refinement.main.number_of_macro_cycles=5 output.prefix="model_refine">

Strangely, the conformations of the MSE residues are changed quite
significantly after refinement in PHENIX, departing both from electron
density and from the prior model. Any help would be appreciated.
Best regards,
Mark A. Wilson
Associate Professor
Department of Biochemistry/Redox Biology Center
University of Nebraska
N118 Beadle Center
1901 Vine Street
Lincoln, NE 68588
(402) 472-3626
mwilson13 at unl.edu 

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