[phenixbb] refinement

Pavel Afonine PAfonine at lbl.gov
Tue Dec 8 18:06:29 PST 2009


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.




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