Hi Xinghua, you can use secondary structure restrains that are available in phenix.refine. It will automatically figure out secondary structure and apply proper restrains. This should preserve your helix geometry and still refine it. Example: phenix.refine model.pdb data.mtz main.secondary_structure_restraints=true

Recently I am trying to fix a helice, but found that it is so hard for me because of the poor resolution(3.2A) and also a unvisible loop near it, so is there any way to just fix a helice ? can I get it out of the whole structure to refine it?

If you still prefer not refining that helix over applying secondary-structure restrains, then you can do that too: phenix.refine model.pdb data.mtz refine.sites.individual="not (chain A and resseq 123:156)" where atom selection chain A and resseq 123:156 selects your helix, and prefix "not" means you exclude it from refinement. Of course you can do all this from PHENIX GUI. Let me know if you have any questions. Pavel.