Forgot to mention: for the Cartesian dynamics the command would be : simulated_annealing=true Pavel. On 12/8/09 6:06 PM, Pavel Afonine wrote:
Hi Pei-Chun,
What command should I use to do Cartesian or torsion-angle simulated annealing?
simulated_annealing_torsion=true
For example:
phenix.refine model.pdb data.mtz your_parameters.params simulated_annealing_torsion=true
If you run it from the GUI, then I guess there will be an obvious check-box for this.
Pavel.
Where should I change if I want to run .eff? } simulated_annealing { start_temperature = 5000 final_temperature = 300 cool_rate = 100 number_of_steps = 25 time_step = 0.0005 n_print = 100 update_grads_shift = 0.3 refine_sites = True refine_adp = False max_number_of_iterations = 25 mode = every_macro_cycle *second_and_before_last once first verbose = -1
The default seatings above look good to me. You may try "aggressive" SA by increasing the start_temperature, say up to 10000K or so. Of course, you need to have a clear idea why to do so in your particular case.
Pavel.