[phenixbb] Shake

Pavel Afonine PAfonine at lbl.gov
Thu Aug 13 14:17:41 PDT 2009


Hi Esmael,

yes, you can shake any selected atoms before the refinement starts:

phenix.refine model.pdb data.hkl sites.shake=0.5 
modify_start_model.selection="sidechain"

or

phenix.refine model.pdb data.hkl sites.shake=0.5 
modify_start_model.selection="backbone"

or

phenix.refine model.pdb data.hkl sites.shake=0.5 
modify_start_model.selection="chain A and resseq 1-100 and not element H"

and so on.

You can do it outside of phenix.refine too:

phenix.pdbtools model.pdb sites.shake=0.5 
modify_start_model.selection="sidechain"

like this you will get a PDB file with the distorted model.

Pavel.



On 8/13/09 2:05 PM, esmael wrote:
> Hi,
>
> Would be possible to only add  "Shake" to the side-chain atoms during  
> the refinement with Phenix?
>
> Thanks,
> Esmael
>
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>   



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