[phenixbb] Cis/trans peptide plane restraints ?

[Nigel Moriarty]

Philippe

You can use

apply_peptide_plane=True

to apply a plane to the atoms so it will be flatter regardless of the
cis/trans configuration.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : NWMoriarty at LBL.gov
Web  : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464


On Mon, Sep 11, 2023 at 7:58 AM CUNIASSE Philippe <Philippe.CUNIASSE at cea.fr>
wrote:

> Dear all,
>
>
>
> I am currently trying to refine a MDFF structure with the phenix
> RealSpaceRefine protocol of phenix.
>
> I am wondering if it is possible to apply systematic restraints to peptide
> plane (in trans when they are trans and cis when they are cis in order to
> avoid twisted conformations of the peptide planes at the end of the
> refinement.
>
> The only possibility I saw is to apply dihedral restraints defined one by
> one but when having thousands of residues, it seems not really convenient.
>
> Thanks in advance for your help.
>
> Best regards.
>
> Philippe.
>
>
>
>
>
> -----------------------------------------------
>
> Philippe Cuniasse, PhD/HDR.
>
> Institut de Biologie Integrative de la cellule.
>
> UMR 9198 CNRS-CEA-Univ Paris Sud
>
> Bat 144 CE-Saclay
>
> 91191 Gif-sur-Yvette Cedex
>
> France
>
> Tel:      (33) 1 69 08 56 35
>
> Fax:      (33) 1 69 08 47 12
>
> Email: philippe.cuniasse at cea.fr
>
> Web: http://biodev.cea.fr/rasmot3d/
>
>
>
> *[image: signature_863913621]*[image: signature_2053578832][image:
> signature_1816548304]
>
> -----------------------------------------------
>
>
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