Shijun

You can ask all the questions you like about Phenix on PhenixBB. However, to answer your question, you can set all peptides to trans using

apply_all_trans=True


or more specific control using

apply_cis_trans_specification {

    cis_trans_mod = cis *trans

    residue_selection = None

  }


to any number of peptides.

Cheers

Nigel

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Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : [log in to unmask]
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Thu, Mar 1, 2018 at 10:58 PM, 张士军 <[log in to unmask]> wrote:

Dear all

   I am refining a structure which has cis-Pro and trans-Pro, the tans-Pro is gone when I set the "threshold degrees for cis-peptide " from default 45 to 65, but still has cis-Pro. While no significant change when I set it to 15. My question is how to set in phenix refinement to clear the Pro residues in cis- or trans- conformations.

Best Regards

shijun