[phenixbb] SA

Pavel Afonine pafonine at lbl.gov
Fri May 1 15:37:17 PDT 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
>
> ------------------------------------------------------------------------
> *От:* Pavel Afonine <pafonine at lbl.gov>
> *Отправлено:* 30 апреля 2015 г. 15:30
> *Кому:* Irina PROKHOROVA; phenixbb at phenix-online.org
> *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

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