[phenixbb] how to fix a secondary structure?

Pavel Afonine pafonine at lbl.gov
Fri Jul 16 22:24:35 PDT 2010

  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.


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.


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