Hello Xiao,

if you use the command line to run programs then the line you quoted illustrates how to change the temperature.

If you are using the GUI, for Cartesian SA:

Refinement settings -> All parameters -> Advanced -> Simulated annealing

for torsion SA:

Refinement settings -> All parameters -> Advanced -> Torsion angle dynamics

This will pop up a window where you can change the default temperature.

Pavel

On 7/13/15 16:50, Xiao Lei wrote:

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