[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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