[phenixbb] refinement

[Pei-Chun Lin]

Hi, I have a question after readng this.

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

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


Thanks for the answer.


PC




> From: rwgk at cci.lbl.gov
> Date: Tue, 8 Dec 2009 12:34:09 -0800
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] refinement
> 
> > I do have very low resolution data (around 4 ang), what are
> > the efficient way of doing refinement, either rigid body alone or
> > rigidbody and tls or individual with group_adp. I did both, but not
> > much significant changes in Rfree stays around 48/50%.
> 
> You could also try Cartesian or torsion-angle simulated annealing.
> I'd try both. In my experience Cartesian SA often works better even
> at low resolution.
> If you get errors running torsion-angle annealing, please try
> the latest nightly build (dev-249) since I've fixed several
> problems since the 1.5-2 release.
> 
> > Also I do have other questions
> >    
> > 1. While doing rigid body refinement, phenix complaint about the
> > special position and could not perform rigid body refinement,
> > whereas individual site refinement is working fine. I do have to
> > delete the atom in special position for rigid body refinement?
> 
> You could use
>   sites.rigid_body = ...
> to select the bodies you want to refine. The rest (including your
> atom on the special position) will not move.
> 
> Ralf
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