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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