Dear Phenixbb members,

I'm learning phenix this days. I use phenix refinement and found there is a simulated annealing option (SA Cartesian or SA torsion option). However, I found the SA cartesian starts at 5000K and SA torsion starts at 2500K by default, and I'd like to change the starting temperature by myself. I search phenix manual and found:

To change starting SA temperature:

% phenix.refine data.hkl model.pdb simulated_annealing=true \
strategy=individual_sites simulated_annealing.start_temperature=10000

I do not understand this, does this mean I have to type the above command in somewhere in phenix? is there a place I can simply put SA start temperature numbers in?

Xiao