[phenixbb] cis-Pro and trans-Pro refinement

Oleg Sobolev osobolev at lbl.gov
Fri Mar 16 10:45:08 PDT 2018

Hi Shijun,

"Threshold degrees for cis-peptide" is only used to determine if Pro is cis
or trans. If you increase this value it is expected that some trans Pro
will become labeled as cis. It does not influence the refinement directly.
If you want to impose restraints and get more trans-Pro after refinement
you may try to use apply_all_trans=True option. But the best would be to
examine carefully the model and map and rebuild appropriate parts manually.

Best regards,
Oleg Sobolev.

On Thu, Mar 1, 2018 at 11:35 PM, 张士军 <21620150150550 at stu.xmu.edu.cn> 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 in phenix GUI to clear
> the Pro residues in cis- or trans- conformations.
> Best Regards
> shijun
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