[phenixbb] Issue with SeMet residues
Pavel Afonine
pafonine at lbl.gov
Thu Nov 7 14:56:46 PST 2013
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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