[phenixbb] cis peptide

[junfeng liu]

Hi Jianghai,
Coot can detect the residues with cis peptides bonds .
Good luck!
liu
Ralf W. Grosse-Kunstleve wrote:
> Hi Jianghai,
>
>   
>> Does phenix.refine restrain cis peptide?
>>     
>
> Yes, controlled via this parameter scope:
>
>     peptide_link {
>       cis_threshold = 45
>       discard_psi_phi = True
>       omega_esd_override_value = None
>     }
>
>   
>> How do I know if the refined
>> pdb file contain any cis peptide?
>>     
>
> In theory you could tell by inspecting the .geo file, but it is difficult
> to pin-point the cis peptide restraints. Probably, it is better to use
> e.g. the pdb deposition tools or something similar to get a listing of
> the cis peptides.
>
> I'll add "list cis peptides" to our to-do list.
>
> Ralf
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>