[phenixbb] probable RTFM question

Pavel Afonine PAfonine at lbl.gov
Thu May 17 12:27:42 PDT 2007

Hi Bill,

it is possible to do but not as straightforward as 
phenix.geometry_minimization.  Example:

% phenix.refine model.pdb data.mtz strategy=individual_sites 
main.bulk_solvent_and_scale=false simulated_annealing=true wxc_scale=0 
--overwrite simulated_annealing.mode=every_macro_cycle

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 
starting temperature.

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:
> Howdie:
> 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.
> Thanks.
> Bill
> William G. Scott
> Contact info:
> http://chemistry.ucsc.edu/~wgscott/
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