[phenixbb] Issue with SeMet residues

[Pavel Afonine]

Real-space refinement is not run by default at this resolution, so no 
need to turn it off explicitly.
Pavel

On 11/7/13 2:53 PM, Nathaniel Echols wrote:
> Try turning off real space refinement:
>
> refine.strategy=individual_sites+individual_adp+occupancies
>
> (and at this resolution, anomalous_group refinement of the seleniums
> would probably also be useful, but you'd have to use the anomalous data
> as input.)
>
> -Nat
>
>
> On Thu, Nov 7, 2013 at 1:12 PM, Mark Wilson <mwilson13 at unl.edu
> <mailto:mwilson13 at unl.edu>> 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 <tel:%28402%29%20472-3626>
>     mwilson13 at unl.edu <mailto:mwilson13 at unl.edu>
>
>
>
>
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