[phenixbb] Simulated annealing

Pavel Afonine PAfonine at lbl.gov
Tue May 12 22:31:54 PDT 2009

Hi Esmael,

- when you run SA it applies to all atoms. It is in my to-do list to 
make it selection sensitive (it is one of the long standing items to fix);

- I'm not sure I understand why don't you like to run it for the whole 
structure? The way it's working in phenix.refine, I wouldn't expect any 
harm. If you try you will see it.


On 5/12/09 9:42 PM, Esmael Haddadian wrote:
> Hi,
> I have tried to only refine the sidechains in my model using the  
> simulated annealing with commands
> strategy=individual_sites
> sites.individual = "sidechain"
> However after the refinement the backbone was also moved; any  
> suggestions as how to only allow sidechain movements during the  
> refinement?
> Thanks,
> Esmael
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