[phenixbb] cis peptide

Jianghai Zhu jzhu at idi.harvard.edu
Sun Nov 9 13:01:42 PST 2008


Thanks, Ralf,

It would be very nice if phenix.refine could output this kind  
information onto the pdb head, just like refmac5 does.  Another  
feature I would like to request is the phase smearing in MLHL  
refinement, which turned out to be very important in one of my recent  
cases.

-- Jianghai






On Nov 8, 2008, at 10:13 PM, 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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