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. Pavel. 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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