[phenixbb] probable RTFM question
PAfonine at lbl.gov
Thu May 17 12:27:42 PDT 2007
it is possible to do but not as straightforward as
% phenix.refine model.pdb data.mtz strategy=individual_sites
main.bulk_solvent_and_scale=false simulated_annealing=true wxc_scale=0
Basically we ask phenix.refine to refine individual coordinates
(strategy=individual_sites), turn off bulk solvent and scaling
(main.bulk_solvent_and_scale=false), tell that we want to do SA
(simulated_annealing=true), turn off X-ray contribution (wxc_scale=0)
and finally ask to do SA every macro-cycle
(simulated_annealing.mode=every_macro_cycle; 3 by default).
This is inefficient (because phenix.refine still calculate all x-ray
targets but not uses them) but currently the only way.
I used this a lot for generating ensembles of models starting from
different random seed. Please note that you may want to play with the
I will add this example to the Manual and I will think about adding
something like phenix.model_anneal in future.
Please let me know if you have any questions.
William Scott wrote:
> I just used phenix.geometry_minimization to try to see the effect of
> deleting some disulphide bonds in a protein structure.
> Is there a way to do the equivalent of CNS's model_anneal (i.e.,
> simulated annealing with just a model)? It wasn't apparent from
> reading the phenix.refine docs.
> William G. Scott
> Contact info:
> phenixbb mailing list
> phenixbb at phenix-online.org
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