Dear Niegel,

May be Shijun had to cancel his registration to the PhenixBB as I had to do since 2015 due to "too many bounces" whatever the email address I used, professional, yahoo or gmail ?... Has this been fixed at some point ?

All the best,
Philippe
 
Philippe BENAS, Ph.D.

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599



De : Nigel Moriarty <[log in to unmask]>
À : [log in to unmask]
Envoyé le : Vendredi 2 mars 2018 8h25
Objet : Re: [ccp4bb] phenix refinement about cis-proline



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

---
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