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.