Re: [phenixbb] SA

1 May 2015

      Hi Irina,

what's the resolution?

Try Cartesian SA instead. Also you can calculate 2mFo-DFc map and run 
real-space refinement - it has large convergence radius.

If the model is more or less in place rigid body refinement may not be 
necessary.

Pavel

On 5/1/15 3:29 PM, Irina PROKHOROVA wrote:
...
Thanks, it worked but not the way I expected.
It definitely found problematic regions in the model but moved it not 
correctly. Should I adjust the parameters of SA? (I did torsion SA 
with a default settings and before MR and rigid-body by domains)
I am still improving the model since it has some clashes. There are 
also disordered regions and tiny movements of big domains. Is it 
neccessary to adjust the model as much as possible with rigid-body 
before SA?
Irina
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*От:* Pavel Afonine 
*Отправлено:* 30 апреля 2015 г. 15:30
*Кому:* Irina PROKHOROVA; [email protected]
*Тема:* Re: [phenixbb] SA
Hi Irina,
SA scope of parameters needs "refinement." prefix:
refinement.simulated_annealing {
    mode = every_macro_cycle second_and_before_last once *first first_half
}
Let me know if it doesn't do it!
Pavel
On 4/30/15 2:20 AM, Irina PROKHOROVA wrote:
...
Hello,
I am trying to run coordinate refinement 5 cycles with first cycle of 
simulated annealing (torsion) via command line. Here is a part of my 
params file that I adapted from my colleges:
refinement.main {
    number_of_macro_cycles = 5
    target = *ml mlhl ml_sad ls
    simulated_annealing_torsion = True
}
simulated_annealing {
    mode = every_macro_cycle second_and_before_last once *first 
first_half
}
refinement.refine {
    strategy = *individual_sites individual_sites_real_space rigid_body \
                individual_adp group_adp tls occupancies group_anomalous
    sites {
      individual = segid *A
      individual = segid *B
    }
As a result I get the Error
...
Unused parameter definitions:
  simulated_annealing.mode (file "refine.params", line 26)
Could you help me with the syntax, please. Should I include sites 
definition for simulated annealing?
Irina