[phenixbb] refinement

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Tue Dec 8 18:09:53 PST 2009

> What command should I use to do Cartesian or torsion-angle simulated
> annealing?


will run Cartesian SA and


will torsion-angle SA. (You can set these in the .def/.eff file
or add them to the command line.)
You'll probably also want

  sites.individual="chain A" sites.torsion_angles="chain A"

or similar.

>   simulated_annealing {
>     start_temperature = 5000
>     ...
>   }

These are the parameters for Cartesian SA.
The torsion-angle SA parameters are in the

  tardy {
    mode = every_macro_cycle *second_and_before_last once first first_half

Sorry it is a bit weird. It is for backward compatibility (for the 1.5-2
release). We are planning to revamp the parameters so it is more
obvious how it works.


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