[phenixbb] Issue with SeMet residues

[Pavel Afonine]

Hi Mark,

it's hard to tell what's happening without looking at files. Could you 
please send me (off mailing list) data.mtz and model.mtz files an I will 
have a look.

Pavel

On 11/7/13 1:12 PM, Mark Wilson wrote:
> 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">
> phenix_refine_1.log
>
>
> 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
>
> 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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